Chlorine in PDB 8b56: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9:
3.4.22.69;
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9, PDB code: 8b56
was solved by
N.Straeter,
C.Mueller,
T.Claff,
K.Sylvester,
R.Weisse,
S.Gao,
L.Song,
X.Liu,
P.Zhan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
56.60 /
1.82
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.833,
99.107,
102.706,
90,
90,
90
|
|
R / Rfree (%)
|
18.5 /
23.1
|
Other elements in 8b56:
The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
(pdb code 8b56). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the
Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9, PDB code: 8b56:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Chlorine binding site 1 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 1 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl401
b:63.1
occ:0.70
|
CL
|
A:OZI401
|
0.0
|
63.1
|
0.7
|
|
CL
|
A:OZI401
|
1.3
|
48.5
|
0.3
|
|
C17
|
A:OZI401
|
1.7
|
46.0
|
0.7
|
|
C17
|
A:OZI401
|
2.6
|
45.1
|
0.3
|
|
C16
|
A:OZI401
|
2.7
|
42.5
|
0.7
|
|
C18
|
A:OZI401
|
2.7
|
43.3
|
0.7
|
|
H21
|
A:OZI401
|
2.8
|
51.2
|
0.7
|
|
HB3
|
A:MET165
|
2.9
|
39.0
|
1.0
|
|
CL1
|
A:OZI401
|
3.1
|
37.5
|
0.7
|
|
HE3
|
A:MET165
|
3.2
|
76.2
|
1.0
|
|
H21
|
A:OZI401
|
3.2
|
53.1
|
0.3
|
|
HA
|
A:ASP187
|
3.3
|
35.0
|
1.0
|
|
C16
|
A:OZI401
|
3.3
|
44.0
|
0.3
|
|
SD
|
A:MET165
|
3.5
|
50.6
|
1.0
|
|
HG2
|
A:GLN189
|
3.6
|
61.8
|
1.0
|
|
C18
|
A:OZI401
|
3.6
|
46.6
|
0.3
|
|
CB
|
A:MET165
|
3.6
|
32.3
|
1.0
|
|
HB2
|
A:MET165
|
3.7
|
39.0
|
1.0
|
|
CE
|
A:MET165
|
3.8
|
63.3
|
1.0
|
|
H
|
A:ARG188
|
3.8
|
33.8
|
1.0
|
|
S
|
A:OZI401
|
3.8
|
49.5
|
0.3
|
|
O
|
A:ARG188
|
3.8
|
29.4
|
1.0
|
|
CL1
|
A:OZI401
|
3.9
|
48.3
|
0.3
|
|
N
|
A:ARG188
|
3.9
|
28.0
|
1.0
|
|
C19
|
A:OZI401
|
4.0
|
46.9
|
0.7
|
|
C15
|
A:OZI401
|
4.0
|
44.5
|
0.7
|
|
HE1
|
A:MET165
|
4.0
|
76.2
|
1.0
|
|
HG3
|
A:GLN189
|
4.0
|
61.8
|
1.0
|
|
C
|
A:ARG188
|
4.0
|
31.6
|
1.0
|
|
CA
|
A:ASP187
|
4.1
|
29.0
|
1.0
|
|
H7
|
A:OZI401
|
4.1
|
65.0
|
0.3
|
|
HE21
|
A:GLN189
|
4.1
|
63.7
|
1.0
|
|
CG
|
A:MET165
|
4.1
|
39.5
|
1.0
|
|
C
|
A:ASP187
|
4.1
|
26.5
|
1.0
|
|
S
|
A:OZI401
|
4.1
|
59.3
|
0.7
|
|
HD2
|
A:HIS41
|
4.2
|
37.4
|
1.0
|
|
CG
|
A:GLN189
|
4.3
|
51.3
|
1.0
|
|
HB2
|
A:ASP187
|
4.3
|
33.6
|
1.0
|
|
C5
|
A:OZI401
|
4.4
|
53.9
|
0.3
|
|
HA
|
A:GLN189
|
4.4
|
46.0
|
1.0
|
|
HG2
|
A:MET165
|
4.4
|
47.6
|
1.0
|
|
CA
|
A:ARG188
|
4.4
|
32.7
|
1.0
|
|
C20
|
A:OZI401
|
4.5
|
46.7
|
0.7
|
|
HA
|
A:ARG188
|
4.5
|
39.5
|
1.0
|
|
O
|
A:VAL186
|
4.6
|
31.3
|
1.0
|
|
CD2
|
A:HIS41
|
4.6
|
30.9
|
1.0
|
|
HE2
|
A:MET165
|
4.6
|
76.2
|
1.0
|
|
N
|
A:GLN189
|
4.6
|
32.1
|
1.0
|
|
C15
|
A:OZI401
|
4.7
|
44.7
|
0.3
|
|
CB
|
A:ASP187
|
4.7
|
27.8
|
1.0
|
|
O
|
A:HIS164
|
4.7
|
28.1
|
1.0
|
|
HE22
|
A:GLN192
|
4.7
|
49.1
|
1.0
|
|
H2
|
A:OZI401
|
4.7
|
58.7
|
0.7
|
|
C19
|
A:OZI401
|
4.8
|
46.2
|
0.3
|
|
NE2
|
A:GLN189
|
4.8
|
52.9
|
1.0
|
|
O
|
A:ASP187
|
4.8
|
31.6
|
1.0
|
|
H22
|
A:OZI401
|
4.9
|
56.5
|
0.7
|
|
HB3
|
A:ASP187
|
4.9
|
33.6
|
1.0
|
|
HB3
|
A:HIS164
|
4.9
|
25.5
|
1.0
|
|
CA
|
A:MET165
|
4.9
|
32.3
|
1.0
|
|
N
|
A:OZI401
|
4.9
|
48.7
|
0.7
|
|
HG3
|
A:MET165
|
4.9
|
47.6
|
1.0
|
|
HA
|
A:MET165
|
5.0
|
39.1
|
1.0
|
|
CA
|
A:GLN189
|
5.0
|
38.1
|
1.0
|
|
C
|
A:OZI401
|
5.0
|
47.5
|
0.7
|
|
Chlorine binding site 2 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 2 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl401
b:48.5
occ:0.30
|
CL
|
A:OZI401
|
0.0
|
48.5
|
0.3
|
|
C17
|
A:OZI401
|
1.1
|
46.0
|
0.7
|
|
CL
|
A:OZI401
|
1.3
|
63.1
|
0.7
|
|
C17
|
A:OZI401
|
1.7
|
45.1
|
0.3
|
|
C18
|
A:OZI401
|
1.9
|
43.3
|
0.7
|
|
C16
|
A:OZI401
|
2.2
|
42.5
|
0.7
|
|
CL1
|
A:OZI401
|
2.6
|
37.5
|
0.7
|
|
H21
|
A:OZI401
|
2.7
|
51.2
|
0.7
|
|
C16
|
A:OZI401
|
2.7
|
44.0
|
0.3
|
|
C18
|
A:OZI401
|
2.7
|
46.6
|
0.3
|
|
H21
|
A:OZI401
|
2.8
|
53.1
|
0.3
|
|
C19
|
A:OZI401
|
3.1
|
46.9
|
0.7
|
|
HD2
|
A:HIS41
|
3.2
|
37.4
|
1.0
|
|
CL1
|
A:OZI401
|
3.2
|
48.3
|
0.3
|
|
HB3
|
A:MET165
|
3.2
|
39.0
|
1.0
|
|
C15
|
A:OZI401
|
3.3
|
44.5
|
0.7
|
|
CD2
|
A:HIS41
|
3.4
|
30.9
|
1.0
|
|
HA
|
A:ASP187
|
3.5
|
35.0
|
1.0
|
|
C20
|
A:OZI401
|
3.6
|
46.7
|
0.7
|
|
HB2
|
A:ASP187
|
3.8
|
33.6
|
1.0
|
|
H22
|
A:OZI401
|
4.0
|
56.5
|
0.7
|
|
NE2
|
A:HIS41
|
4.0
|
29.7
|
1.0
|
|
CG
|
A:HIS41
|
4.0
|
31.2
|
1.0
|
|
C19
|
A:OZI401
|
4.0
|
46.2
|
0.3
|
|
C15
|
A:OZI401
|
4.0
|
44.7
|
0.3
|
|
HG2
|
A:GLN189
|
4.1
|
61.8
|
1.0
|
|
HE2
|
A:HIS41
|
4.1
|
35.9
|
1.0
|
|
HB3
|
A:HIS41
|
4.2
|
36.7
|
1.0
|
|
CB
|
A:MET165
|
4.2
|
32.3
|
1.0
|
|
CA
|
A:ASP187
|
4.2
|
29.0
|
1.0
|
|
HE21
|
A:GLN189
|
4.2
|
63.7
|
1.0
|
|
C
|
A:ASP187
|
4.2
|
26.5
|
1.0
|
|
HG3
|
A:GLN189
|
4.2
|
61.8
|
1.0
|
|
O
|
A:HIS164
|
4.3
|
28.1
|
1.0
|
|
HB2
|
A:HIS41
|
4.3
|
36.7
|
1.0
|
|
N
|
A:ARG188
|
4.3
|
28.0
|
1.0
|
|
HB2
|
A:MET165
|
4.4
|
39.0
|
1.0
|
|
HE3
|
A:MET165
|
4.4
|
76.2
|
1.0
|
|
CB
|
A:ASP187
|
4.4
|
27.8
|
1.0
|
|
SD
|
A:MET165
|
4.4
|
50.6
|
1.0
|
|
CB
|
A:HIS41
|
4.4
|
30.4
|
1.0
|
|
H
|
A:ARG188
|
4.5
|
33.8
|
1.0
|
|
C20
|
A:OZI401
|
4.5
|
45.6
|
0.3
|
|
HB3
|
A:HIS164
|
4.5
|
25.5
|
1.0
|
|
N3
|
A:OZI401
|
4.6
|
45.7
|
0.7
|
|
S
|
A:OZI401
|
4.6
|
49.5
|
0.3
|
|
H
|
A:OZI401
|
4.6
|
52.0
|
0.7
|
|
CG
|
A:GLN189
|
4.6
|
51.3
|
1.0
|
|
HB3
|
A:ASP187
|
4.6
|
33.6
|
1.0
|
|
H2
|
A:OZI401
|
4.7
|
58.7
|
0.7
|
|
O
|
A:ASP187
|
4.7
|
31.6
|
1.0
|
|
ND1
|
A:HIS41
|
4.7
|
31.9
|
1.0
|
|
CE1
|
A:HIS41
|
4.7
|
34.4
|
1.0
|
|
H23
|
A:OZI401
|
4.7
|
56.3
|
0.7
|
|
H
|
A:OZI401
|
4.7
|
52.9
|
0.3
|
|
CG
|
A:MET165
|
4.8
|
39.5
|
1.0
|
|
HA
|
A:ARG188
|
4.8
|
39.5
|
1.0
|
|
C
|
A:ARG188
|
4.8
|
31.6
|
1.0
|
|
O
|
A:ARG188
|
4.8
|
29.4
|
1.0
|
|
H22
|
A:OZI401
|
4.9
|
55.7
|
0.3
|
|
HG2
|
A:MET165
|
4.9
|
47.6
|
1.0
|
|
NE2
|
A:GLN189
|
4.9
|
52.9
|
1.0
|
|
CA
|
A:ARG188
|
4.9
|
32.7
|
1.0
|
|
CE
|
A:MET165
|
4.9
|
63.3
|
1.0
|
|
C6
|
A:OZI401
|
5.0
|
43.1
|
0.7
|
|
Chlorine binding site 3 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 3 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl401
b:37.5
occ:0.70
|
CL1
|
A:OZI401
|
0.0
|
37.5
|
0.7
|
|
CL1
|
A:OZI401
|
1.2
|
48.3
|
0.3
|
|
C18
|
A:OZI401
|
1.7
|
43.3
|
0.7
|
|
C18
|
A:OZI401
|
2.4
|
46.6
|
0.3
|
|
CL
|
A:OZI401
|
2.6
|
48.5
|
0.3
|
|
C19
|
A:OZI401
|
2.7
|
46.9
|
0.7
|
|
C17
|
A:OZI401
|
2.7
|
46.0
|
0.7
|
|
C17
|
A:OZI401
|
2.8
|
45.1
|
0.3
|
|
H22
|
A:OZI401
|
2.8
|
56.5
|
0.7
|
|
HA
|
A:ARG188
|
3.1
|
39.5
|
1.0
|
|
CL
|
A:OZI401
|
3.1
|
63.1
|
0.7
|
|
HG3
|
A:GLN189
|
3.3
|
61.8
|
1.0
|
|
O
|
A:ASP187
|
3.3
|
31.6
|
1.0
|
|
HB2
|
A:HIS41
|
3.3
|
36.7
|
1.0
|
|
HH
|
A:TYR54
|
3.4
|
38.3
|
1.0
|
|
HB3
|
A:HIS41
|
3.5
|
36.7
|
1.0
|
|
HG
|
A:CYS44
|
3.5
|
71.8
|
1.0
|
|
C
|
A:ASP187
|
3.5
|
26.5
|
1.0
|
|
C19
|
A:OZI401
|
3.6
|
46.2
|
0.3
|
|
N
|
A:ARG188
|
3.7
|
28.0
|
1.0
|
|
OH
|
A:TYR54
|
3.7
|
31.7
|
1.0
|
|
CA
|
A:ARG188
|
3.7
|
32.7
|
1.0
|
|
CB
|
A:HIS41
|
3.8
|
30.4
|
1.0
|
|
HB2
|
A:ASP187
|
3.9
|
33.6
|
1.0
|
|
H22
|
A:OZI401
|
3.9
|
55.7
|
0.3
|
|
C20
|
A:OZI401
|
4.0
|
46.7
|
0.7
|
|
C16
|
A:OZI401
|
4.0
|
42.5
|
0.7
|
|
O
|
A:MET49
|
4.0
|
37.1
|
1.0
|
|
C
|
A:ARG188
|
4.1
|
31.6
|
1.0
|
|
HA
|
A:ASP187
|
4.1
|
35.0
|
1.0
|
|
CG
|
A:GLN189
|
4.1
|
51.3
|
1.0
|
|
HG3
|
A:PRO52
|
4.1
|
44.3
|
1.0
|
|
HG2
|
A:GLN189
|
4.1
|
61.8
|
1.0
|
|
H
|
A:GLN189
|
4.2
|
38.8
|
1.0
|
|
C16
|
A:OZI401
|
4.2
|
44.0
|
0.3
|
|
N
|
A:GLN189
|
4.2
|
32.1
|
1.0
|
|
H
|
A:ARG188
|
4.3
|
33.8
|
1.0
|
|
CG
|
A:HIS41
|
4.3
|
31.2
|
1.0
|
|
HD2
|
A:HIS41
|
4.3
|
37.4
|
1.0
|
|
CA
|
A:ASP187
|
4.3
|
29.0
|
1.0
|
|
HA
|
A:MET49
|
4.4
|
65.3
|
1.0
|
|
CD2
|
A:HIS41
|
4.5
|
30.9
|
1.0
|
|
C15
|
A:OZI401
|
4.5
|
44.5
|
0.7
|
|
CB
|
A:ASP187
|
4.6
|
27.8
|
1.0
|
|
SG
|
A:CYS44
|
4.6
|
59.6
|
1.0
|
|
O
|
A:ARG188
|
4.7
|
29.4
|
1.0
|
|
HE21
|
A:GLN189
|
4.8
|
63.7
|
1.0
|
|
C20
|
A:OZI401
|
4.8
|
45.6
|
0.3
|
|
HB3
|
A:MET49
|
4.8
|
75.9
|
1.0
|
|
H23
|
A:OZI401
|
4.8
|
56.3
|
0.7
|
|
H21
|
A:OZI401
|
4.9
|
51.2
|
0.7
|
|
H21
|
A:OZI401
|
4.9
|
53.1
|
0.3
|
|
CD
|
A:GLN189
|
4.9
|
50.1
|
1.0
|
|
C
|
A:MET49
|
5.0
|
42.1
|
1.0
|
|
Chlorine binding site 4 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 4 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl401
b:48.3
occ:0.30
|
CL1
|
A:OZI401
|
0.0
|
48.3
|
0.3
|
|
CL1
|
A:OZI401
|
1.2
|
37.5
|
0.7
|
|
C18
|
A:OZI401
|
1.6
|
43.3
|
0.7
|
|
C18
|
A:OZI401
|
1.7
|
46.6
|
0.3
|
|
H22
|
A:OZI401
|
1.8
|
56.5
|
0.7
|
|
C19
|
A:OZI401
|
1.9
|
46.9
|
0.7
|
|
C19
|
A:OZI401
|
2.7
|
46.2
|
0.3
|
|
C17
|
A:OZI401
|
2.7
|
45.1
|
0.3
|
|
H22
|
A:OZI401
|
2.8
|
55.7
|
0.3
|
|
C17
|
A:OZI401
|
2.9
|
46.0
|
0.7
|
|
HG
|
A:CYS44
|
3.0
|
71.8
|
1.0
|
|
HG3
|
A:GLN189
|
3.1
|
61.8
|
1.0
|
|
HB2
|
A:HIS41
|
3.1
|
36.7
|
1.0
|
|
CL
|
A:OZI401
|
3.2
|
48.5
|
0.3
|
|
C20
|
A:OZI401
|
3.3
|
46.7
|
0.7
|
|
HA
|
A:MET49
|
3.6
|
65.3
|
1.0
|
|
HB3
|
A:HIS41
|
3.7
|
36.7
|
1.0
|
|
CB
|
A:HIS41
|
3.8
|
30.4
|
1.0
|
|
HA
|
A:ARG188
|
3.9
|
39.5
|
1.0
|
|
CL
|
A:OZI401
|
3.9
|
63.1
|
0.7
|
|
O
|
A:MET49
|
3.9
|
37.1
|
1.0
|
|
SD
|
A:MET49
|
3.9
|
71.4
|
1.0
|
|
CG
|
A:GLN189
|
3.9
|
51.3
|
1.0
|
|
C20
|
A:OZI401
|
4.0
|
45.6
|
0.3
|
|
C16
|
A:OZI401
|
4.0
|
42.5
|
0.7
|
|
H23
|
A:OZI401
|
4.0
|
56.3
|
0.7
|
|
C16
|
A:OZI401
|
4.0
|
44.0
|
0.3
|
|
HB3
|
A:MET49
|
4.0
|
75.9
|
1.0
|
|
HH
|
A:TYR54
|
4.1
|
38.3
|
1.0
|
|
HG2
|
A:GLN189
|
4.1
|
61.8
|
1.0
|
|
SG
|
A:CYS44
|
4.1
|
59.6
|
1.0
|
|
C15
|
A:OZI401
|
4.1
|
44.5
|
0.7
|
|
OH
|
A:TYR54
|
4.2
|
31.7
|
1.0
|
|
HG3
|
A:PRO52
|
4.3
|
44.3
|
1.0
|
|
CG
|
A:HIS41
|
4.3
|
31.2
|
1.0
|
|
O
|
A:ASP187
|
4.3
|
31.6
|
1.0
|
|
CD
|
A:GLN189
|
4.4
|
50.1
|
1.0
|
|
CA
|
A:MET49
|
4.4
|
54.2
|
1.0
|
|
HB2
|
A:CYS44
|
4.4
|
62.2
|
1.0
|
|
HE21
|
A:GLN189
|
4.4
|
63.7
|
1.0
|
|
H
|
A:GLN189
|
4.4
|
38.8
|
1.0
|
|
C15
|
A:OZI401
|
4.5
|
44.7
|
0.3
|
|
NE2
|
A:GLN189
|
4.6
|
52.9
|
1.0
|
|
CA
|
A:ARG188
|
4.6
|
32.7
|
1.0
|
|
CB
|
A:MET49
|
4.6
|
63.0
|
1.0
|
|
C
|
A:MET49
|
4.6
|
42.1
|
1.0
|
|
C
|
A:ASP187
|
4.6
|
26.5
|
1.0
|
|
HB3
|
A:CYS44
|
4.6
|
62.2
|
1.0
|
|
N
|
A:GLN189
|
4.6
|
32.1
|
1.0
|
|
CB
|
A:CYS44
|
4.7
|
51.6
|
1.0
|
|
CD2
|
A:HIS41
|
4.7
|
30.9
|
1.0
|
|
C
|
A:ARG188
|
4.8
|
31.6
|
1.0
|
|
N
|
A:ARG188
|
4.8
|
28.0
|
1.0
|
|
HD2
|
A:HIS41
|
4.8
|
37.4
|
1.0
|
|
H23
|
A:OZI401
|
4.8
|
55.0
|
0.3
|
|
H21
|
A:OZI401
|
4.9
|
53.1
|
0.3
|
|
HB2
|
A:ASP187
|
4.9
|
33.6
|
1.0
|
|
CG
|
A:MET49
|
4.9
|
70.2
|
1.0
|
|
ND1
|
A:HIS41
|
4.9
|
31.9
|
1.0
|
|
H21
|
A:OZI401
|
5.0
|
51.2
|
0.7
|
|
HA
|
A:HIS41
|
5.0
|
34.9
|
1.0
|
|
Chlorine binding site 5 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 5 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl401
b:58.9
occ:0.70
|
CL
|
B:OZI401
|
0.0
|
58.9
|
0.7
|
|
CL
|
B:OZI401
|
0.6
|
57.2
|
0.3
|
|
C17
|
B:OZI401
|
1.7
|
56.3
|
0.7
|
|
C17
|
B:OZI401
|
2.0
|
56.1
|
0.3
|
|
HE3
|
B:MET165
|
2.3
|
64.0
|
1.0
|
|
C16
|
B:OZI401
|
2.7
|
56.0
|
0.7
|
|
C18
|
B:OZI401
|
2.7
|
58.2
|
0.7
|
|
C18
|
B:OZI401
|
2.8
|
58.8
|
0.3
|
|
H21
|
B:OZI401
|
2.8
|
67.4
|
0.7
|
|
CE
|
B:MET165
|
3.0
|
53.1
|
1.0
|
|
CL1
|
B:OZI401
|
3.0
|
62.7
|
0.3
|
|
HE2
|
B:MET165
|
3.0
|
64.0
|
1.0
|
|
C16
|
B:OZI401
|
3.0
|
55.4
|
0.3
|
|
HB3
|
B:MET165
|
3.1
|
55.0
|
1.0
|
|
CL1
|
B:OZI401
|
3.2
|
63.0
|
0.7
|
|
H21
|
B:OZI401
|
3.2
|
66.8
|
0.3
|
|
HE1
|
B:MET165
|
3.2
|
64.0
|
1.0
|
|
HA
|
B:ASP187
|
3.3
|
50.0
|
1.0
|
|
HB2
|
B:ASP187
|
3.8
|
49.8
|
1.0
|
|
N
|
B:ARG188
|
3.9
|
49.2
|
1.0
|
|
HD2
|
B:HIS41
|
3.9
|
52.1
|
1.0
|
|
C
|
B:ASP187
|
3.9
|
48.3
|
1.0
|
|
CA
|
B:ASP187
|
4.0
|
41.5
|
1.0
|
|
S
|
B:OZI401
|
4.0
|
60.5
|
0.3
|
|
C15
|
B:OZI401
|
4.0
|
55.7
|
0.7
|
|
C19
|
B:OZI401
|
4.0
|
61.0
|
0.7
|
|
H
|
B:ARG188
|
4.0
|
59.3
|
1.0
|
|
CB
|
B:MET165
|
4.0
|
45.6
|
1.0
|
|
O
|
B:ARG188
|
4.0
|
55.4
|
1.0
|
|
C19
|
B:OZI401
|
4.1
|
60.5
|
0.3
|
|
HB2
|
B:MET165
|
4.1
|
55.0
|
1.0
|
|
C
|
B:ARG188
|
4.1
|
61.5
|
1.0
|
|
HA
|
B:ARG188
|
4.1
|
74.0
|
1.0
|
|
S
|
B:OZI401
|
4.1
|
64.7
|
0.7
|
|
HG2
|
B:GLN189
|
4.1
|
89.0
|
1.0
|
|
CD2
|
B:HIS41
|
4.1
|
43.2
|
1.0
|
|
H7
|
B:OZI401
|
4.2
|
83.6
|
0.3
|
|
C15
|
B:OZI401
|
4.3
|
55.3
|
0.3
|
|
CA
|
B:ARG188
|
4.3
|
61.4
|
1.0
|
|
CB
|
B:ASP187
|
4.3
|
41.2
|
1.0
|
|
C5
|
B:OZI401
|
4.4
|
69.5
|
0.3
|
|
HG3
|
B:GLN189
|
4.4
|
89.0
|
1.0
|
|
C20
|
B:OZI401
|
4.5
|
59.5
|
0.7
|
|
O
|
B:ASP187
|
4.5
|
54.7
|
1.0
|
|
SD
|
B:MET165
|
4.5
|
56.9
|
1.0
|
|
HB3
|
B:ASP187
|
4.6
|
49.8
|
1.0
|
|
O
|
B:HIS164
|
4.6
|
38.9
|
1.0
|
|
N
|
B:GLN189
|
4.6
|
72.8
|
1.0
|
|
CG
|
B:HIS41
|
4.6
|
45.3
|
1.0
|
|
HB3
|
B:HIS41
|
4.7
|
59.2
|
1.0
|
|
C20
|
B:OZI401
|
4.7
|
58.4
|
0.3
|
|
NE2
|
B:HIS41
|
4.7
|
41.8
|
1.0
|
|
H2
|
B:OZI401
|
4.7
|
68.7
|
0.7
|
|
CG
|
B:MET165
|
4.7
|
46.8
|
1.0
|
|
HA
|
B:GLN189
|
4.8
|
101.5
|
1.0
|
|
CG
|
B:GLN189
|
4.8
|
73.9
|
1.0
|
|
HB2
|
B:HIS41
|
4.8
|
59.2
|
1.0
|
|
HB3
|
B:HIS164
|
4.8
|
46.8
|
1.0
|
|
HE2
|
B:HIS41
|
4.8
|
50.4
|
1.0
|
|
H22
|
B:OZI401
|
4.8
|
73.5
|
0.7
|
|
O
|
B:VAL186
|
4.8
|
41.1
|
1.0
|
|
H
|
B:OZI401
|
4.9
|
61.5
|
0.7
|
|
H22
|
B:OZI401
|
4.9
|
72.9
|
0.3
|
|
C5
|
B:OZI401
|
4.9
|
73.5
|
0.7
|
|
HE21
|
B:GLN189
|
4.9
|
85.4
|
1.0
|
|
H7
|
B:OZI401
|
4.9
|
88.4
|
0.7
|
|
HA
|
B:MET165
|
4.9
|
51.1
|
1.0
|
|
HG2
|
B:MET165
|
4.9
|
56.4
|
1.0
|
|
H
|
B:GLN189
|
5.0
|
87.7
|
1.0
|
|
CB
|
B:HIS41
|
5.0
|
49.1
|
1.0
|
|
N
|
B:OZI401
|
5.0
|
57.0
|
0.7
|
|
Chlorine binding site 6 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 6 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl401
b:57.2
occ:0.30
|
CL
|
B:OZI401
|
0.0
|
57.2
|
0.3
|
|
CL
|
B:OZI401
|
0.6
|
58.9
|
0.7
|
|
C17
|
B:OZI401
|
1.6
|
56.3
|
0.7
|
|
C17
|
B:OZI401
|
1.7
|
56.1
|
0.3
|
|
C16
|
B:OZI401
|
2.4
|
56.0
|
0.7
|
|
HE3
|
B:MET165
|
2.4
|
64.0
|
1.0
|
|
H21
|
B:OZI401
|
2.5
|
67.4
|
0.7
|
|
C16
|
B:OZI401
|
2.7
|
55.4
|
0.3
|
|
C18
|
B:OZI401
|
2.7
|
58.2
|
0.7
|
|
C18
|
B:OZI401
|
2.7
|
58.8
|
0.3
|
|
H21
|
B:OZI401
|
2.8
|
66.8
|
0.3
|
|
HB3
|
B:MET165
|
2.8
|
55.0
|
1.0
|
|
CL1
|
B:OZI401
|
3.2
|
62.7
|
0.3
|
|
CE
|
B:MET165
|
3.2
|
53.1
|
1.0
|
|
HE2
|
B:MET165
|
3.2
|
64.0
|
1.0
|
|
CL1
|
B:OZI401
|
3.4
|
63.0
|
0.7
|
|
HD2
|
B:HIS41
|
3.4
|
52.1
|
1.0
|
|
HA
|
B:ASP187
|
3.5
|
50.0
|
1.0
|
|
HE1
|
B:MET165
|
3.6
|
64.0
|
1.0
|
|
CD2
|
B:HIS41
|
3.7
|
43.2
|
1.0
|
|
C15
|
B:OZI401
|
3.7
|
55.7
|
0.7
|
|
CB
|
B:MET165
|
3.8
|
45.6
|
1.0
|
|
HB2
|
B:ASP187
|
3.8
|
49.8
|
1.0
|
|
C19
|
B:OZI401
|
3.9
|
61.0
|
0.7
|
|
HB2
|
B:MET165
|
4.0
|
55.0
|
1.0
|
|
C15
|
B:OZI401
|
4.0
|
55.3
|
0.3
|
|
C19
|
B:OZI401
|
4.0
|
60.5
|
0.3
|
|
O
|
B:HIS164
|
4.0
|
38.9
|
1.0
|
|
S
|
B:OZI401
|
4.1
|
60.5
|
0.3
|
|
NE2
|
B:HIS41
|
4.1
|
41.8
|
1.0
|
|
CA
|
B:ASP187
|
4.2
|
41.5
|
1.0
|
|
CG
|
B:HIS41
|
4.2
|
45.3
|
1.0
|
|
HE2
|
B:HIS41
|
4.2
|
50.4
|
1.0
|
|
C
|
B:ASP187
|
4.3
|
48.3
|
1.0
|
|
C20
|
B:OZI401
|
4.3
|
59.5
|
0.7
|
|
S
|
B:OZI401
|
4.3
|
64.7
|
0.7
|
|
N
|
B:ARG188
|
4.4
|
49.2
|
1.0
|
|
CB
|
B:ASP187
|
4.4
|
41.2
|
1.0
|
|
HB3
|
B:HIS164
|
4.4
|
46.8
|
1.0
|
|
H
|
B:OZI401
|
4.4
|
61.5
|
0.7
|
|
HB3
|
B:HIS41
|
4.5
|
59.2
|
1.0
|
|
C20
|
B:OZI401
|
4.5
|
58.4
|
0.3
|
|
H
|
B:ARG188
|
4.5
|
59.3
|
1.0
|
|
HB3
|
B:ASP187
|
4.5
|
49.8
|
1.0
|
|
HG2
|
B:GLN189
|
4.5
|
89.0
|
1.0
|
|
HA
|
B:MET165
|
4.5
|
51.1
|
1.0
|
|
CG
|
B:MET165
|
4.6
|
46.8
|
1.0
|
|
H7
|
B:OZI401
|
4.6
|
83.6
|
0.3
|
|
SD
|
B:MET165
|
4.6
|
56.9
|
1.0
|
|
HA
|
B:ARG188
|
4.6
|
74.0
|
1.0
|
|
H2
|
B:OZI401
|
4.6
|
68.7
|
0.7
|
|
HB2
|
B:HIS41
|
4.6
|
59.2
|
1.0
|
|
O
|
B:ARG188
|
4.6
|
55.4
|
1.0
|
|
CA
|
B:MET165
|
4.7
|
42.3
|
1.0
|
|
H
|
B:OZI401
|
4.7
|
61.6
|
0.3
|
|
HG2
|
B:MET165
|
4.7
|
56.4
|
1.0
|
|
C
|
B:ARG188
|
4.7
|
61.5
|
1.0
|
|
C5
|
B:OZI401
|
4.7
|
69.5
|
0.3
|
|
CB
|
B:HIS41
|
4.7
|
49.1
|
1.0
|
|
C
|
B:HIS164
|
4.7
|
38.2
|
1.0
|
|
N3
|
B:OZI401
|
4.8
|
53.9
|
0.7
|
|
H22
|
B:OZI401
|
4.8
|
73.5
|
0.7
|
|
HG3
|
B:GLN189
|
4.8
|
89.0
|
1.0
|
|
CE1
|
B:HIS41
|
4.8
|
49.3
|
1.0
|
|
O
|
B:ASP187
|
4.8
|
54.7
|
1.0
|
|
CA
|
B:ARG188
|
4.8
|
61.4
|
1.0
|
|
H22
|
B:OZI401
|
4.9
|
72.9
|
0.3
|
|
N
|
B:OZI401
|
4.9
|
57.0
|
0.7
|
|
C
|
B:OZI401
|
4.9
|
51.5
|
0.7
|
|
ND1
|
B:HIS41
|
4.9
|
50.2
|
1.0
|
|
C6
|
B:OZI401
|
4.9
|
51.0
|
0.7
|
|
Chlorine binding site 7 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 7 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl401
b:63.0
occ:0.70
|
CL1
|
B:OZI401
|
0.0
|
63.0
|
0.7
|
|
CL1
|
B:OZI401
|
0.3
|
62.7
|
0.3
|
|
C18
|
B:OZI401
|
1.8
|
58.2
|
0.7
|
|
C18
|
B:OZI401
|
2.1
|
58.8
|
0.3
|
|
C19
|
B:OZI401
|
2.7
|
61.0
|
0.7
|
|
C17
|
B:OZI401
|
2.7
|
56.3
|
0.7
|
|
H22
|
B:OZI401
|
2.8
|
73.5
|
0.7
|
|
HB2
|
B:HIS41
|
2.8
|
59.2
|
1.0
|
|
HA
|
B:ARG188
|
3.0
|
74.0
|
1.0
|
|
C19
|
B:OZI401
|
3.0
|
60.5
|
0.3
|
|
C17
|
B:OZI401
|
3.0
|
56.1
|
0.3
|
|
H22
|
B:OZI401
|
3.0
|
72.9
|
0.3
|
|
CL
|
B:OZI401
|
3.2
|
58.9
|
0.7
|
|
HG3
|
B:MET49
|
3.2
|
115.1
|
1.0
|
|
HB3
|
B:HIS41
|
3.3
|
59.2
|
1.0
|
|
CL
|
B:OZI401
|
3.4
|
57.2
|
0.3
|
|
CB
|
B:HIS41
|
3.5
|
49.1
|
1.0
|
|
HH
|
B:TYR54
|
3.5
|
63.1
|
1.0
|
|
O
|
B:ASP187
|
3.5
|
54.7
|
1.0
|
|
OH
|
B:TYR54
|
3.6
|
52.4
|
1.0
|
|
HG3
|
B:GLN189
|
3.7
|
89.0
|
1.0
|
|
CA
|
B:ARG188
|
3.8
|
61.4
|
1.0
|
|
C
|
B:ASP187
|
3.8
|
48.3
|
1.0
|
|
C20
|
B:OZI401
|
4.0
|
59.5
|
0.7
|
|
C16
|
B:OZI401
|
4.0
|
56.0
|
0.7
|
|
CG
|
B:HIS41
|
4.0
|
45.3
|
1.0
|
|
HB2
|
B:ASP187
|
4.0
|
49.8
|
1.0
|
|
H
|
B:GLN189
|
4.0
|
87.7
|
1.0
|
|
N
|
B:ARG188
|
4.1
|
49.2
|
1.0
|
|
CG
|
B:MET49
|
4.2
|
95.7
|
1.0
|
|
HA
|
B:MET49
|
4.2
|
105.8
|
1.0
|
|
C
|
B:ARG188
|
4.3
|
61.5
|
1.0
|
|
HG2
|
B:MET49
|
4.3
|
115.1
|
1.0
|
|
N
|
B:GLN189
|
4.3
|
72.8
|
1.0
|
|
C20
|
B:OZI401
|
4.3
|
58.4
|
0.3
|
|
C16
|
B:OZI401
|
4.3
|
55.4
|
0.3
|
|
SG
|
B:CYS44
|
4.4
|
73.7
|
1.0
|
|
O
|
B:MET49
|
4.4
|
82.6
|
1.0
|
|
HG2
|
B:PRO52
|
4.4
|
90.8
|
1.0
|
|
HD2
|
B:HIS41
|
4.5
|
52.1
|
1.0
|
|
CD2
|
B:HIS41
|
4.5
|
43.2
|
1.0
|
|
HB2
|
B:CYS44
|
4.5
|
77.9
|
1.0
|
|
C15
|
B:OZI401
|
4.5
|
55.7
|
0.7
|
|
CG
|
B:GLN189
|
4.6
|
73.9
|
1.0
|
|
HG2
|
B:GLN189
|
4.6
|
89.0
|
1.0
|
|
HG3
|
B:PRO52
|
4.6
|
90.8
|
1.0
|
|
HA
|
B:HIS41
|
4.7
|
51.6
|
1.0
|
|
HA
|
B:ASP187
|
4.7
|
50.0
|
1.0
|
|
H
|
B:ARG188
|
4.7
|
59.3
|
1.0
|
|
CA
|
B:HIS41
|
4.7
|
42.8
|
1.0
|
|
CA
|
B:ASP187
|
4.7
|
41.5
|
1.0
|
|
ND1
|
B:HIS41
|
4.8
|
50.2
|
1.0
|
|
CB
|
B:ASP187
|
4.8
|
41.2
|
1.0
|
|
HB3
|
B:CYS44
|
4.8
|
77.9
|
1.0
|
|
H23
|
B:OZI401
|
4.8
|
71.7
|
0.7
|
|
CB
|
B:CYS44
|
4.9
|
64.7
|
1.0
|
|
C15
|
B:OZI401
|
4.9
|
55.3
|
0.3
|
|
H21
|
B:OZI401
|
4.9
|
67.4
|
0.7
|
|
HB3
|
B:ARG188
|
4.9
|
80.8
|
1.0
|
|
CZ
|
B:TYR54
|
4.9
|
52.7
|
1.0
|
|
CB
|
B:ARG188
|
5.0
|
67.1
|
1.0
|
|
CA
|
B:MET49
|
5.0
|
88.0
|
1.0
|
|
Chlorine binding site 8 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 8 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl401
b:62.7
occ:0.30
|
CL1
|
B:OZI401
|
0.0
|
62.7
|
0.3
|
|
CL1
|
B:OZI401
|
0.3
|
63.0
|
0.7
|
|
C18
|
B:OZI401
|
1.4
|
58.2
|
0.7
|
|
C18
|
B:OZI401
|
1.7
|
58.8
|
0.3
|
|
C19
|
B:OZI401
|
2.4
|
61.0
|
0.7
|
|
C17
|
B:OZI401
|
2.4
|
56.3
|
0.7
|
|
H22
|
B:OZI401
|
2.6
|
73.5
|
0.7
|
|
C19
|
B:OZI401
|
2.7
|
60.5
|
0.3
|
|
C17
|
B:OZI401
|
2.7
|
56.1
|
0.3
|
|
H22
|
B:OZI401
|
2.8
|
72.9
|
0.3
|
|
HB2
|
B:HIS41
|
2.8
|
59.2
|
1.0
|
|
CL
|
B:OZI401
|
3.0
|
58.9
|
0.7
|
|
CL
|
B:OZI401
|
3.2
|
57.2
|
0.3
|
|
HA
|
B:ARG188
|
3.2
|
74.0
|
1.0
|
|
HG3
|
B:MET49
|
3.2
|
115.1
|
1.0
|
|
HB3
|
B:HIS41
|
3.3
|
59.2
|
1.0
|
|
CB
|
B:HIS41
|
3.5
|
49.1
|
1.0
|
|
HG3
|
B:GLN189
|
3.6
|
89.0
|
1.0
|
|
C20
|
B:OZI401
|
3.7
|
59.5
|
0.7
|
|
C16
|
B:OZI401
|
3.7
|
56.0
|
0.7
|
|
O
|
B:ASP187
|
3.8
|
54.7
|
1.0
|
|
HH
|
B:TYR54
|
3.8
|
63.1
|
1.0
|
|
OH
|
B:TYR54
|
3.9
|
52.4
|
1.0
|
|
CG
|
B:HIS41
|
3.9
|
45.3
|
1.0
|
|
CA
|
B:ARG188
|
4.0
|
61.4
|
1.0
|
|
C20
|
B:OZI401
|
4.0
|
58.4
|
0.3
|
|
C16
|
B:OZI401
|
4.0
|
55.4
|
0.3
|
|
C
|
B:ASP187
|
4.0
|
48.3
|
1.0
|
|
CG
|
B:MET49
|
4.1
|
95.7
|
1.0
|
|
H
|
B:GLN189
|
4.1
|
87.7
|
1.0
|
|
HB2
|
B:ASP187
|
4.2
|
49.8
|
1.0
|
|
HG2
|
B:MET49
|
4.2
|
115.1
|
1.0
|
|
C15
|
B:OZI401
|
4.2
|
55.7
|
0.7
|
|
N
|
B:ARG188
|
4.2
|
49.2
|
1.0
|
|
C
|
B:ARG188
|
4.3
|
61.5
|
1.0
|
|
N
|
B:GLN189
|
4.3
|
72.8
|
1.0
|
|
CD2
|
B:HIS41
|
4.4
|
43.2
|
1.0
|
|
HG2
|
B:GLN189
|
4.4
|
89.0
|
1.0
|
|
HA
|
B:MET49
|
4.4
|
105.8
|
1.0
|
|
CG
|
B:GLN189
|
4.4
|
73.9
|
1.0
|
|
HD2
|
B:HIS41
|
4.4
|
52.1
|
1.0
|
|
C15
|
B:OZI401
|
4.5
|
55.3
|
0.3
|
|
H23
|
B:OZI401
|
4.5
|
71.7
|
0.7
|
|
HB2
|
B:CYS44
|
4.5
|
77.9
|
1.0
|
|
H21
|
B:OZI401
|
4.6
|
67.4
|
0.7
|
|
SG
|
B:CYS44
|
4.6
|
73.7
|
1.0
|
|
O
|
B:MET49
|
4.6
|
82.6
|
1.0
|
|
ND1
|
B:HIS41
|
4.6
|
50.2
|
1.0
|
|
HA
|
B:HIS41
|
4.8
|
51.6
|
1.0
|
|
HG2
|
B:PRO52
|
4.8
|
90.8
|
1.0
|
|
CA
|
B:HIS41
|
4.8
|
42.8
|
1.0
|
|
HA
|
B:ASP187
|
4.8
|
50.0
|
1.0
|
|
H23
|
B:OZI401
|
4.8
|
70.4
|
0.3
|
|
H21
|
B:OZI401
|
4.9
|
66.8
|
0.3
|
|
H
|
B:ARG188
|
4.9
|
59.3
|
1.0
|
|
CA
|
B:ASP187
|
4.9
|
41.5
|
1.0
|
|
HB3
|
B:CYS44
|
4.9
|
77.9
|
1.0
|
|
HG3
|
B:PRO52
|
4.9
|
90.8
|
1.0
|
|
CB
|
B:CYS44
|
4.9
|
64.7
|
1.0
|
|
CB
|
B:ASP187
|
5.0
|
41.2
|
1.0
|
|
HE21
|
B:GLN189
|
5.0
|
85.4
|
1.0
|
|
Chlorine binding site 9 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 9 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl402
b:46.0
occ:1.00
|
H
|
A:ALA285
|
2.5
|
58.9
|
1.0
|
|
H
|
B:ALA285
|
2.6
|
55.6
|
1.0
|
|
H
|
A:LEU286
|
3.2
|
56.6
|
1.0
|
|
HB3
|
A:SER284
|
3.3
|
46.9
|
1.0
|
|
N
|
A:ALA285
|
3.3
|
48.8
|
1.0
|
|
OG
|
B:SER284
|
3.3
|
66.6
|
1.0
|
|
HA
|
B:SER284
|
3.3
|
51.4
|
1.0
|
|
H
|
B:LEU286
|
3.4
|
58.1
|
1.0
|
|
N
|
B:ALA285
|
3.4
|
46.1
|
1.0
|
|
HA
|
A:SER284
|
3.4
|
51.0
|
1.0
|
|
HB3
|
A:ALA285
|
3.5
|
60.2
|
1.0
|
|
O
|
A:HOH585
|
3.6
|
54.8
|
1.0
|
|
HB2
|
A:LEU286
|
3.7
|
57.1
|
1.0
|
|
HB3
|
B:ALA285
|
3.8
|
58.9
|
1.0
|
|
HG
|
B:SER284
|
3.8
|
80.2
|
1.0
|
|
N
|
A:LEU286
|
3.8
|
47.0
|
1.0
|
|
HB2
|
B:LEU286
|
3.8
|
61.1
|
1.0
|
|
HG
|
B:LEU286
|
3.9
|
71.2
|
1.0
|
|
N
|
B:LEU286
|
4.0
|
48.2
|
1.0
|
|
HG
|
A:LEU286
|
4.0
|
76.6
|
1.0
|
|
CA
|
A:SER284
|
4.0
|
42.3
|
1.0
|
|
CA
|
B:SER284
|
4.0
|
42.6
|
1.0
|
|
HD12
|
B:LEU286
|
4.0
|
71.6
|
1.0
|
|
HD12
|
A:LEU286
|
4.0
|
73.5
|
1.0
|
|
CB
|
A:SER284
|
4.1
|
38.9
|
1.0
|
|
CA
|
A:ALA285
|
4.1
|
45.5
|
1.0
|
|
C
|
A:SER284
|
4.2
|
46.2
|
1.0
|
|
CB
|
B:SER284
|
4.2
|
48.5
|
1.0
|
|
CB
|
A:ALA285
|
4.2
|
49.9
|
1.0
|
|
C
|
A:ALA285
|
4.2
|
48.7
|
1.0
|
|
C
|
B:SER284
|
4.2
|
43.9
|
1.0
|
|
CA
|
B:ALA285
|
4.3
|
49.3
|
1.0
|
|
CB
|
A:LEU286
|
4.4
|
47.4
|
1.0
|
|
HB2
|
B:SER284
|
4.5
|
58.5
|
1.0
|
|
C
|
B:ALA285
|
4.5
|
51.7
|
1.0
|
|
CB
|
B:ALA285
|
4.5
|
48.8
|
1.0
|
|
CB
|
B:LEU286
|
4.5
|
50.7
|
1.0
|
|
CG
|
B:LEU286
|
4.5
|
59.1
|
1.0
|
|
CG
|
A:LEU286
|
4.5
|
63.6
|
1.0
|
|
HB2
|
A:ALA285
|
4.6
|
60.2
|
1.0
|
|
CA
|
A:LEU286
|
4.7
|
42.0
|
1.0
|
|
CD1
|
B:LEU286
|
4.7
|
59.5
|
1.0
|
|
CD1
|
A:LEU286
|
4.7
|
61.0
|
1.0
|
|
HB2
|
A:SER284
|
4.7
|
46.9
|
1.0
|
|
OG
|
A:SER284
|
4.8
|
63.6
|
1.0
|
|
HB2
|
B:ALA285
|
4.9
|
58.9
|
1.0
|
|
CA
|
B:LEU286
|
4.9
|
54.0
|
1.0
|
|
HA
|
A:ALA285
|
5.0
|
54.8
|
1.0
|
|
HB1
|
A:ALA285
|
5.0
|
60.2
|
1.0
|
|
Chlorine binding site 10 out
of 10 in 8b56
Go back to
Chlorine Binding Sites List in 8b56
Chlorine binding site 10 out
of 10 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 10 of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) in Complex with the Inhibitor Gd-9 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl403
b:56.8
occ:1.00
|
HH11
|
B:ARG4
|
2.7
|
53.7
|
1.0
|
|
H
|
B:LYS5
|
2.9
|
40.7
|
1.0
|
|
HD3
|
B:ARG4
|
2.9
|
48.2
|
1.0
|
|
HZ2
|
A:LYS5
|
3.1
|
69.6
|
1.0
|
|
O
|
B:HOH537
|
3.3
|
40.0
|
1.0
|
|
HG2
|
A:LYS5
|
3.3
|
56.5
|
1.0
|
|
NH1
|
B:ARG4
|
3.5
|
44.5
|
1.0
|
|
HB3
|
B:LYS5
|
3.5
|
38.2
|
1.0
|
|
HB2
|
B:LYS5
|
3.6
|
38.2
|
1.0
|
|
HD2
|
B:ARG4
|
3.7
|
48.2
|
1.0
|
|
N
|
B:LYS5
|
3.7
|
33.7
|
1.0
|
|
CD
|
B:ARG4
|
3.7
|
39.9
|
1.0
|
|
HH12
|
B:ARG4
|
3.8
|
53.7
|
1.0
|
|
HA
|
B:ARG4
|
3.8
|
39.1
|
1.0
|
|
NZ
|
A:LYS5
|
3.9
|
57.7
|
1.0
|
|
CB
|
B:LYS5
|
3.9
|
31.6
|
1.0
|
|
HB3
|
B:ARG4
|
4.1
|
39.4
|
1.0
|
|
HZ3
|
A:LYS5
|
4.2
|
69.6
|
1.0
|
|
CG
|
A:LYS5
|
4.3
|
46.8
|
1.0
|
|
HZ1
|
A:LYS5
|
4.3
|
69.6
|
1.0
|
|
CA
|
B:LYS5
|
4.4
|
36.7
|
1.0
|
|
CZ
|
B:ARG4
|
4.4
|
35.5
|
1.0
|
|
HB3
|
A:LYS5
|
4.5
|
54.1
|
1.0
|
|
CA
|
B:ARG4
|
4.5
|
32.4
|
1.0
|
|
NE
|
B:ARG4
|
4.5
|
35.8
|
1.0
|
|
CB
|
B:ARG4
|
4.6
|
32.6
|
1.0
|
|
C
|
B:ARG4
|
4.6
|
30.1
|
1.0
|
|
O
|
B:LYS5
|
4.6
|
39.2
|
1.0
|
|
HG3
|
A:LYS5
|
4.7
|
56.5
|
1.0
|
|
CG
|
B:ARG4
|
4.7
|
36.8
|
1.0
|
|
HB2
|
A:LYS5
|
4.8
|
54.1
|
1.0
|
|
CB
|
A:LYS5
|
4.8
|
44.9
|
1.0
|
|
CE
|
A:LYS5
|
4.8
|
52.0
|
1.0
|
|
HE3
|
A:LYS5
|
4.9
|
62.6
|
1.0
|
|
O
|
A:GLN127
|
5.0
|
34.7
|
1.0
|
|
C
|
B:LYS5
|
5.0
|
34.1
|
1.0
|
|
Reference:
S.Gao,
L.Song,
T.Claff,
M.Woodson,
K.Sylvester,
L.Jing,
R.H.Weisse,
Y.Cheng,
N.Strater,
L.Schakel,
M.Gutschow,
B.Ye,
M.Yang,
T.Zhang,
D.Kang,
K.Toth,
J.Tavis,
A.E.Tollefson,
C.E.Muller,
P.Zhan,
X.Liu.
Discovery and Crystallographic Studies of Nonpeptidic Piperazine Derivatives As Covalent Sars-Cov-2 Main Protease Inhibitors. J.Med.Chem. V. 65 16902 2022.
ISSN: ISSN 0022-2623
PubMed: 36475694
DOI: 10.1021/ACS.JMEDCHEM.2C01716
Page generated: Thu Dec 28 03:02:14 2023
|
