Chlorine in PDB 7e47: Crystal Structure of Compound 6 Bound to Mif
Enzymatic activity of Crystal Structure of Compound 6 Bound to Mif
All present enzymatic activity of Crystal Structure of Compound 6 Bound to Mif:
5.3.2.1;
5.3.3.12;
Protein crystallography data
The structure of Crystal Structure of Compound 6 Bound to Mif, PDB code: 7e47
was solved by
C.P.Fan,
L.Yang,
D.Y.Guo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.11 /
1.38
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.388,
67.713,
88.224,
90,
90,
90
|
R / Rfree (%)
|
15.4 /
17.9
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Compound 6 Bound to Mif
(pdb code 7e47). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Crystal Structure of Compound 6 Bound to Mif, PDB code: 7e47:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 1 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:18.3
occ:1.00
|
O
|
C:HOH329
|
3.0
|
18.1
|
1.0
|
N
|
A:ASN102
|
3.1
|
13.6
|
1.0
|
ND2
|
A:ASN105
|
3.2
|
16.4
|
1.0
|
CG
|
A:ASN102
|
3.7
|
21.8
|
1.0
|
CB
|
A:ASN102
|
3.8
|
16.9
|
1.0
|
CA
|
A:MET101
|
3.9
|
13.3
|
1.0
|
O
|
A:HOH387
|
3.9
|
25.3
|
1.0
|
CB
|
A:ASN105
|
3.9
|
14.2
|
1.0
|
C
|
A:MET101
|
4.0
|
13.9
|
1.0
|
CG
|
A:ASN105
|
4.0
|
15.6
|
1.0
|
ND2
|
A:ASN102
|
4.0
|
24.5
|
1.0
|
CA
|
A:ASN102
|
4.1
|
14.5
|
1.0
|
O
|
C:HOH406
|
4.1
|
22.6
|
1.0
|
CE
|
A:MET101
|
4.1
|
17.1
|
1.0
|
OD1
|
A:ASN102
|
4.1
|
24.8
|
1.0
|
O
|
A:ASP100
|
4.2
|
15.1
|
1.0
|
SD
|
A:MET101
|
4.3
|
17.2
|
1.0
|
CB
|
A:MET101
|
4.5
|
14.1
|
1.0
|
O
|
C:HOH357
|
4.5
|
23.0
|
1.0
|
O
|
A:HOH307
|
4.5
|
23.0
|
1.0
|
O
|
A:ASN102
|
4.7
|
13.8
|
1.0
|
O
|
C:HOH407
|
4.7
|
40.4
|
1.0
|
O
|
A:HOH313
|
4.8
|
33.5
|
1.0
|
N
|
A:MET101
|
4.9
|
13.5
|
1.0
|
C
|
A:ASN102
|
4.9
|
14.1
|
1.0
|
O
|
C:TYR98
|
4.9
|
14.4
|
1.0
|
C
|
A:ASP100
|
5.0
|
14.2
|
1.0
|
O
|
A:HOH396
|
5.0
|
23.8
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 2 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:26.7
occ:1.00
|
N
|
A:PRO1
|
3.2
|
15.0
|
1.0
|
N
|
A:ILE64
|
3.2
|
14.2
|
1.0
|
CD
|
A:PRO1
|
3.4
|
16.3
|
1.0
|
O
|
A:HOH305
|
3.4
|
36.9
|
1.0
|
CA
|
A:PRO1
|
3.6
|
14.1
|
1.0
|
CG
|
A:PRO1
|
3.7
|
16.8
|
1.0
|
O
|
A:HOH405
|
3.7
|
25.8
|
1.0
|
CG1
|
A:ILE64
|
3.8
|
15.9
|
1.0
|
CB
|
A:ILE64
|
3.8
|
14.6
|
1.0
|
CA
|
A:SER63
|
3.9
|
13.3
|
1.0
|
CD1
|
A:ILE64
|
4.0
|
17.4
|
1.0
|
C
|
A:SER63
|
4.0
|
14.2
|
1.0
|
CA
|
A:ILE64
|
4.1
|
14.6
|
1.0
|
OG
|
A:SER63
|
4.2
|
15.8
|
1.0
|
CB
|
A:PRO1
|
4.3
|
15.6
|
1.0
|
CE
|
A:LYS32
|
4.3
|
24.3
|
1.0
|
NZ
|
A:LYS32
|
4.5
|
28.1
|
1.0
|
CD
|
A:LYS32
|
4.5
|
24.5
|
1.0
|
CB
|
A:SER63
|
4.7
|
15.0
|
1.0
|
O
|
A:ILE64
|
4.8
|
16.4
|
1.0
|
O
|
A:HIS62
|
4.9
|
14.0
|
1.0
|
C
|
A:ILE64
|
4.9
|
14.6
|
1.0
|
C
|
A:PRO1
|
4.9
|
12.9
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 3 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl201
b:17.5
occ:1.00
|
O
|
B:HOH376
|
3.1
|
33.8
|
1.0
|
O
|
A:HOH326
|
3.1
|
16.5
|
1.0
|
N
|
B:ASN102
|
3.1
|
15.3
|
1.0
|
ND2
|
B:ASN105
|
3.2
|
16.1
|
1.0
|
O
|
B:HOH384
|
3.3
|
36.6
|
1.0
|
CG
|
B:ASN102
|
3.8
|
22.4
|
1.0
|
CB
|
B:ASN102
|
3.8
|
16.6
|
1.0
|
CA
|
B:MET101
|
3.8
|
14.0
|
1.0
|
CB
|
B:ASN105
|
3.9
|
14.1
|
1.0
|
CE
|
B:MET101
|
3.9
|
17.9
|
1.0
|
C
|
B:MET101
|
4.0
|
15.1
|
1.0
|
O
|
B:HOH366
|
4.0
|
23.0
|
1.0
|
CG
|
B:ASN105
|
4.0
|
15.7
|
1.0
|
ND2
|
B:ASN102
|
4.0
|
26.3
|
1.0
|
O
|
A:HOH433
|
4.0
|
21.8
|
1.0
|
CA
|
B:ASN102
|
4.1
|
15.0
|
1.0
|
OD1
|
B:ASN102
|
4.1
|
25.7
|
1.0
|
O
|
B:ASP100
|
4.2
|
17.0
|
1.0
|
SD
|
B:MET101
|
4.3
|
17.8
|
1.0
|
CB
|
B:MET101
|
4.5
|
14.6
|
1.0
|
O
|
B:HOH302
|
4.6
|
21.8
|
1.0
|
O
|
B:ASN102
|
4.6
|
14.6
|
1.0
|
O
|
A:HOH364
|
4.7
|
19.8
|
1.0
|
O
|
A:HOH435
|
4.7
|
31.8
|
1.0
|
C
|
B:ASN102
|
4.9
|
13.9
|
1.0
|
N
|
B:MET101
|
4.9
|
14.1
|
1.0
|
O
|
B:HOH305
|
4.9
|
36.0
|
1.0
|
O
|
A:TYR98
|
5.0
|
13.4
|
1.0
|
C
|
B:ASP100
|
5.0
|
15.7
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 4 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl202
b:29.8
occ:1.00
|
N
|
B:PRO1
|
3.1
|
16.7
|
1.0
|
N
|
B:ILE64
|
3.3
|
14.8
|
1.0
|
CD
|
B:PRO1
|
3.3
|
19.0
|
1.0
|
O
|
B:HOH313
|
3.5
|
30.9
|
1.0
|
O
|
B:HOH374
|
3.7
|
25.1
|
1.0
|
CA
|
B:PRO1
|
3.7
|
15.8
|
1.0
|
CG
|
B:PRO1
|
3.7
|
18.4
|
1.0
|
CG1
|
B:ILE64
|
3.7
|
17.3
|
1.0
|
CB
|
B:ILE64
|
3.8
|
16.3
|
1.0
|
CD1
|
B:ILE64
|
3.9
|
17.1
|
1.0
|
CA
|
B:SER63
|
4.0
|
14.5
|
1.0
|
C
|
B:SER63
|
4.1
|
14.8
|
1.0
|
CA
|
B:ILE64
|
4.1
|
15.7
|
1.0
|
OG
|
B:SER63
|
4.2
|
17.1
|
1.0
|
CB
|
B:PRO1
|
4.3
|
16.9
|
1.0
|
CE
|
B:LYS32
|
4.4
|
26.1
|
1.0
|
CD
|
B:LYS32
|
4.6
|
26.8
|
1.0
|
NZ
|
B:LYS32
|
4.7
|
26.7
|
1.0
|
CB
|
B:SER63
|
4.7
|
15.2
|
1.0
|
O
|
B:ILE64
|
4.8
|
18.1
|
1.0
|
O
|
B:HIS62
|
4.9
|
15.9
|
1.0
|
C
|
B:ILE64
|
4.9
|
16.3
|
1.0
|
C
|
B:PRO1
|
5.0
|
15.3
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 5 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl203
b:37.7
occ:1.00
|
NE2
|
B:GLN71
|
3.2
|
26.8
|
1.0
|
N
|
B:GLN71
|
3.3
|
22.7
|
1.0
|
N
|
B:ALA70
|
3.5
|
24.3
|
1.0
|
C
|
B:GLY68
|
3.5
|
20.8
|
1.0
|
CA
|
B:GLY68
|
3.6
|
18.8
|
1.0
|
CG
|
B:GLN71
|
3.6
|
23.4
|
1.0
|
N
|
B:GLY69
|
3.6
|
22.4
|
1.0
|
CB
|
B:GLN71
|
3.9
|
20.3
|
1.0
|
CD
|
B:GLN71
|
3.9
|
24.9
|
1.0
|
O
|
B:GLY68
|
4.0
|
20.2
|
1.0
|
CB
|
B:ALA70
|
4.0
|
24.7
|
1.0
|
CA
|
B:ALA70
|
4.1
|
24.2
|
1.0
|
C
|
B:ALA70
|
4.2
|
23.4
|
1.0
|
CA
|
B:GLN71
|
4.2
|
19.8
|
1.0
|
N
|
B:GLY68
|
4.2
|
19.4
|
1.0
|
C
|
B:GLY69
|
4.3
|
22.3
|
1.0
|
CA
|
B:GLY69
|
4.4
|
23.1
|
1.0
|
C
|
B:ILE67
|
4.9
|
20.2
|
1.0
|
O
|
B:ILE67
|
5.0
|
23.4
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 6 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl201
b:20.1
occ:1.00
|
O
|
B:HOH323
|
3.0
|
16.0
|
1.0
|
N
|
C:ASN102
|
3.1
|
16.4
|
1.0
|
ND2
|
C:ASN105
|
3.2
|
19.1
|
1.0
|
O
|
C:HOH398
|
3.3
|
42.3
|
1.0
|
CB
|
C:ASN102
|
3.7
|
20.2
|
1.0
|
CG
|
C:ASN102
|
3.8
|
24.9
|
1.0
|
CA
|
C:MET101
|
3.8
|
15.2
|
1.0
|
CB
|
C:ASN105
|
3.9
|
16.6
|
1.0
|
C
|
C:MET101
|
4.0
|
15.2
|
1.0
|
O
|
C:HOH369
|
4.0
|
30.2
|
1.0
|
CG
|
C:ASN105
|
4.0
|
18.1
|
1.0
|
CA
|
C:ASN102
|
4.1
|
18.2
|
1.0
|
CE
|
C:MET101
|
4.1
|
18.9
|
1.0
|
O
|
B:HOH405
|
4.1
|
21.8
|
1.0
|
OD1
|
C:ASN102
|
4.1
|
28.7
|
1.0
|
ND2
|
C:ASN102
|
4.1
|
29.3
|
1.0
|
O
|
C:ASP100
|
4.2
|
17.5
|
1.0
|
SD
|
C:MET101
|
4.3
|
18.6
|
1.0
|
CB
|
C:MET101
|
4.6
|
15.8
|
1.0
|
O
|
B:HOH348
|
4.6
|
19.1
|
1.0
|
O
|
C:ASN102
|
4.6
|
17.1
|
1.0
|
O
|
B:HOH403
|
4.8
|
31.5
|
1.0
|
O
|
C:HOH317
|
4.8
|
45.1
|
1.0
|
N
|
C:MET101
|
4.8
|
15.5
|
1.0
|
C
|
C:ASN102
|
4.9
|
18.1
|
1.0
|
C
|
C:ASP100
|
5.0
|
15.2
|
1.0
|
O
|
B:TYR98
|
5.0
|
15.3
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 7e47
Go back to
Chlorine Binding Sites List in 7e47
Chlorine binding site 7 out
of 7 in the Crystal Structure of Compound 6 Bound to Mif
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 Compound 6 Bound to Mif within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl202
b:31.6
occ:1.00
|
OG
|
C:SER63
|
2.9
|
22.3
|
1.0
|
N
|
C:PRO1
|
3.1
|
16.9
|
1.0
|
CE
|
C:LYS32
|
3.4
|
30.3
|
1.0
|
CA
|
C:PRO1
|
3.5
|
15.8
|
1.0
|
C19
|
C:HWR203
|
3.5
|
17.2
|
1.0
|
CB
|
C:SER63
|
3.6
|
18.6
|
1.0
|
CA
|
C:SER63
|
3.6
|
15.1
|
1.0
|
N
|
C:ILE64
|
3.7
|
15.5
|
1.0
|
CG
|
C:LYS32
|
3.8
|
24.6
|
1.0
|
CD
|
C:PRO1
|
3.9
|
18.3
|
1.0
|
C20
|
C:HWR203
|
4.0
|
18.3
|
1.0
|
CD
|
C:LYS32
|
4.0
|
29.2
|
1.0
|
C22
|
C:HWR203
|
4.1
|
16.6
|
1.0
|
O6
|
C:HWR203
|
4.1
|
19.0
|
1.0
|
CB
|
C:PRO1
|
4.2
|
17.9
|
1.0
|
C
|
C:SER63
|
4.2
|
17.1
|
1.0
|
O5
|
C:HWR203
|
4.3
|
16.4
|
1.0
|
C15
|
C:HWR203
|
4.4
|
17.3
|
1.0
|
C18
|
C:HWR203
|
4.5
|
17.0
|
1.0
|
NZ
|
C:LYS32
|
4.5
|
28.8
|
1.0
|
O
|
C:ILE64
|
4.6
|
25.2
|
1.0
|
C16
|
C:HWR203
|
4.6
|
17.5
|
1.0
|
O
|
C:HIS62
|
4.6
|
14.6
|
1.0
|
CG
|
C:PRO1
|
4.6
|
19.3
|
1.0
|
C21
|
C:HWR203
|
4.7
|
15.3
|
1.0
|
C
|
C:PRO1
|
4.8
|
15.4
|
1.0
|
CB
|
C:LYS32
|
4.8
|
23.1
|
1.0
|
CA
|
C:ILE64
|
4.8
|
16.8
|
1.0
|
C14
|
C:HWR203
|
4.9
|
17.4
|
1.0
|
N
|
C:SER63
|
4.9
|
14.0
|
1.0
|
C
|
C:ILE64
|
5.0
|
22.4
|
1.0
|
|
Reference:
L.Yang,
D.Guo,
C.Fan.
Identification and Structure-Activity Relationships of Dietary Flavonoids As Human Macrophage Migration Inhibitory Factor (Mif) Inhibitors. J.Agric.Food Chem. V. 69 10138 2021.
ISSN: ESSN 1520-5118
PubMed: 34459191
DOI: 10.1021/ACS.JAFC.1C03367
Page generated: Mon Jul 29 20:23:17 2024
|