Chlorine in PDB 8pxg: Structure of Streptactin, Solved at Wavelength 2.75 A
Protein crystallography data
The structure of Structure of Streptactin, Solved at Wavelength 2.75 A, PDB code: 8pxg
was solved by
K.El Omari,
R.Duman,
V.Mykhaylyk,
C.Orr,
L.Vecchia,
E.Y.Jones,
A.Wagner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.47 /
1.80
|
Space group
|
I 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.42,
57.42,
172.05,
90,
90,
90
|
R / Rfree (%)
|
17.4 /
19.4
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of Streptactin, Solved at Wavelength 2.75 A
(pdb code 8pxg). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Structure of Streptactin, Solved at Wavelength 2.75 A, PDB code: 8pxg:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 1 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl201
b:41.4
occ:1.00
|
ND2
|
A:ASN106
|
3.3
|
42.5
|
1.0
|
N
|
A:THR103
|
3.4
|
32.3
|
1.0
|
CA
|
A:THR102
|
3.6
|
29.0
|
1.0
|
CB
|
A:THR102
|
3.7
|
29.0
|
1.0
|
OG1
|
A:THR103
|
3.8
|
35.6
|
1.0
|
CB
|
A:ASN106
|
3.9
|
37.4
|
1.0
|
CG2
|
A:THR103
|
4.0
|
37.0
|
1.0
|
C
|
A:THR102
|
4.0
|
31.3
|
1.0
|
CG
|
A:ASN106
|
4.1
|
41.4
|
1.0
|
CG2
|
A:THR102
|
4.3
|
28.7
|
1.0
|
CB
|
A:THR103
|
4.3
|
36.2
|
1.0
|
CA
|
A:THR103
|
4.4
|
34.2
|
1.0
|
O
|
A:GLY101
|
4.6
|
29.6
|
1.0
|
N
|
A:THR102
|
4.9
|
27.9
|
1.0
|
OG1
|
A:THR102
|
4.9
|
28.1
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 2 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl202
b:40.3
occ:1.00
|
OH
|
A:TYR31
|
2.7
|
19.0
|
1.0
|
O3
|
A:GOL208
|
2.8
|
28.9
|
1.0
|
O
|
A:HOH362
|
3.0
|
48.9
|
1.0
|
OG
|
A:SER15
|
3.0
|
25.2
|
1.0
|
O
|
A:HOH358
|
3.2
|
29.0
|
1.0
|
CB
|
A:SER15
|
3.5
|
23.5
|
1.0
|
ND2
|
A:ASN11
|
3.5
|
25.8
|
1.0
|
CZ
|
A:TYR31
|
3.6
|
17.5
|
1.0
|
C3
|
A:GOL208
|
3.6
|
29.0
|
1.0
|
CE1
|
A:TYR31
|
3.6
|
17.8
|
1.0
|
O2
|
A:GOL208
|
3.8
|
30.4
|
1.0
|
O
|
A:HOH352
|
4.1
|
43.1
|
1.0
|
C2
|
A:GOL208
|
4.3
|
28.5
|
1.0
|
OD2
|
A:ASP116
|
4.4
|
22.0
|
1.0
|
CG
|
A:ASN11
|
4.6
|
23.1
|
1.0
|
CZ2
|
A:TRP80
|
4.6
|
16.8
|
1.0
|
CE2
|
A:TYR31
|
4.9
|
17.1
|
1.0
|
CD1
|
A:TYR31
|
4.9
|
16.9
|
1.0
|
CA
|
A:SER15
|
4.9
|
21.8
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 3 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl203
b:32.2
occ:1.00
|
OD1
|
A:ASP116
|
3.1
|
28.2
|
1.0
|
N
|
A:GLN12
|
3.2
|
26.3
|
1.0
|
N
|
A:THR117
|
3.3
|
18.8
|
1.0
|
CA
|
A:ASP116
|
3.5
|
18.8
|
1.0
|
CB
|
A:GLN12
|
3.6
|
32.6
|
1.0
|
CB
|
A:ASN11
|
3.7
|
21.7
|
1.0
|
CG
|
A:GLN12
|
3.7
|
33.5
|
1.0
|
O
|
A:THR117
|
3.8
|
18.0
|
1.0
|
C
|
A:ASP116
|
3.9
|
18.2
|
1.0
|
CA
|
A:GLN12
|
3.9
|
30.7
|
1.0
|
CG
|
A:ASP116
|
3.9
|
22.0
|
1.0
|
CB
|
A:ASP116
|
4.0
|
19.2
|
1.0
|
CG
|
A:ASN11
|
4.2
|
23.1
|
1.0
|
C
|
A:ASN11
|
4.2
|
24.0
|
1.0
|
ND2
|
A:ASN11
|
4.2
|
25.8
|
1.0
|
CA
|
A:ASN11
|
4.2
|
21.1
|
1.0
|
CA
|
A:THR117
|
4.3
|
19.1
|
1.0
|
O
|
A:HIS115
|
4.4
|
19.4
|
1.0
|
C
|
A:THR117
|
4.4
|
18.1
|
1.0
|
CG
|
A:LEU13
|
4.5
|
42.3
|
1.0
|
C
|
A:GLN12
|
4.6
|
33.2
|
1.0
|
CD1
|
A:LEU13
|
4.6
|
43.6
|
1.0
|
N
|
A:LEU13
|
4.6
|
33.9
|
1.0
|
N
|
A:ASP116
|
4.7
|
17.7
|
1.0
|
CL
|
A:CL204
|
4.8
|
44.2
|
1.0
|
CB
|
A:THR117
|
4.8
|
22.4
|
1.0
|
CD
|
A:GLN12
|
4.9
|
35.0
|
1.0
|
OD1
|
A:ASN11
|
5.0
|
22.8
|
1.0
|
O
|
A:HOH329
|
5.0
|
32.3
|
1.0
|
C
|
A:HIS115
|
5.0
|
18.8
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 4 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl204
b:44.2
occ:1.00
|
OG1
|
A:THR117
|
2.8
|
24.0
|
1.0
|
ND1
|
A:HIS115
|
2.9
|
23.9
|
1.0
|
N
|
A:THR117
|
3.4
|
18.8
|
1.0
|
C
|
A:ASP116
|
3.5
|
18.2
|
1.0
|
N
|
A:ASP116
|
3.8
|
17.7
|
1.0
|
CG
|
A:HIS115
|
3.8
|
22.6
|
1.0
|
CA
|
A:ASP116
|
3.8
|
18.8
|
1.0
|
C
|
A:HIS115
|
3.9
|
18.8
|
1.0
|
CB
|
A:HIS115
|
3.9
|
20.6
|
1.0
|
CE1
|
A:HIS115
|
3.9
|
25.6
|
1.0
|
CB
|
A:THR117
|
3.9
|
22.4
|
1.0
|
O
|
A:ASP116
|
4.0
|
17.7
|
1.0
|
O
|
A:HIS115
|
4.1
|
19.4
|
1.0
|
CA
|
A:THR117
|
4.2
|
19.1
|
1.0
|
CA
|
A:HIS115
|
4.5
|
18.0
|
1.0
|
CL
|
A:CL203
|
4.8
|
32.2
|
1.0
|
O
|
A:THR94
|
4.9
|
17.2
|
1.0
|
CD2
|
A:HIS115
|
5.0
|
24.3
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 5 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl205
b:33.4
occ:1.00
|
N
|
A:ASP24
|
2.9
|
30.6
|
1.0
|
O
|
A:HOH346
|
3.1
|
33.4
|
1.0
|
C
|
A:ASP24
|
3.3
|
26.5
|
1.0
|
CA
|
A:ASP24
|
3.4
|
30.8
|
1.0
|
N
|
A:ALA26
|
3.4
|
18.9
|
1.0
|
C
|
A:GLY22
|
3.4
|
26.7
|
1.0
|
CB
|
A:ALA26
|
3.5
|
19.9
|
1.0
|
N
|
A:ALA23
|
3.5
|
29.3
|
1.0
|
N
|
A:GLY25
|
3.5
|
22.6
|
1.0
|
CA
|
A:GLY22
|
3.6
|
24.2
|
1.0
|
CB
|
A:ASP24
|
3.7
|
34.6
|
1.0
|
O
|
A:ASP24
|
3.8
|
27.7
|
1.0
|
O
|
A:GLY22
|
3.9
|
26.9
|
1.0
|
C
|
A:ALA23
|
4.0
|
33.4
|
1.0
|
CA
|
A:ALA26
|
4.1
|
18.8
|
1.0
|
CA
|
A:ALA23
|
4.3
|
32.1
|
1.0
|
C
|
A:GLY25
|
4.5
|
19.2
|
1.0
|
CA
|
A:GLY25
|
4.6
|
20.7
|
1.0
|
N
|
A:GLY22
|
4.6
|
22.4
|
1.0
|
CG
|
A:ASP24
|
4.6
|
39.8
|
1.0
|
O
|
A:HOH357
|
4.6
|
36.7
|
1.0
|
OD2
|
A:ASP24
|
4.8
|
44.3
|
1.0
|
O
|
A:ALA26
|
5.0
|
19.3
|
1.0
|
NH1
|
A:ARG47
|
5.0
|
20.4
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 6 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl206
b:44.6
occ:1.00
|
N
|
A:ASN70
|
3.2
|
19.7
|
1.0
|
CB
|
A:ASN69
|
3.5
|
16.9
|
1.0
|
CB
|
A:ASN70
|
3.6
|
24.9
|
1.0
|
O
|
A:HOH350
|
3.7
|
40.7
|
1.0
|
CG
|
A:ASN70
|
3.8
|
27.7
|
1.0
|
ND2
|
A:ASN70
|
3.8
|
31.6
|
1.0
|
CG
|
A:ASN69
|
3.9
|
17.0
|
1.0
|
CA
|
A:ASN70
|
3.9
|
21.5
|
1.0
|
O
|
A:ALA38
|
4.0
|
32.5
|
1.0
|
CD1
|
A:TYR71
|
4.0
|
24.7
|
1.0
|
CE1
|
A:TYR71
|
4.2
|
26.7
|
1.0
|
C
|
A:ASN69
|
4.2
|
18.7
|
1.0
|
ND2
|
A:ASN69
|
4.2
|
17.1
|
1.0
|
CA
|
A:ASN69
|
4.2
|
17.3
|
1.0
|
O
|
A:ARG41
|
4.4
|
17.7
|
1.0
|
OD1
|
A:ASN69
|
4.4
|
17.5
|
1.0
|
OD1
|
A:ASN70
|
4.6
|
29.9
|
1.0
|
N
|
A:TYR71
|
4.8
|
19.4
|
1.0
|
C
|
A:ASN70
|
4.8
|
20.6
|
1.0
|
C
|
A:ALA38
|
4.9
|
36.3
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 8pxg
Go back to
Chlorine Binding Sites List in 8pxg
Chlorine binding site 7 out
of 7 in the Structure of Streptactin, Solved at Wavelength 2.75 A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Structure of Streptactin, Solved at Wavelength 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl207
b:39.3
occ:1.00
|
OH
|
A:TYR42
|
2.8
|
17.0
|
1.0
|
OG1
|
A:THR33
|
3.0
|
24.6
|
1.0
|
NH2
|
A:ARG72
|
3.5
|
29.5
|
0.5
|
CE1
|
A:TYR42
|
3.6
|
15.4
|
1.0
|
CZ
|
A:TYR42
|
3.7
|
16.1
|
1.0
|
CG2
|
A:THR33
|
3.9
|
23.3
|
1.0
|
O
|
A:HOH326
|
3.9
|
45.3
|
1.0
|
CB
|
A:THR33
|
3.9
|
24.3
|
1.0
|
CA
|
A:SER40
|
4.0
|
24.8
|
1.0
|
O
|
A:GLU39
|
4.1
|
26.8
|
1.0
|
CD
|
A:ARG72
|
4.3
|
24.2
|
0.5
|
OG
|
A:SER40
|
4.4
|
31.0
|
1.0
|
CB
|
A:SER40
|
4.4
|
26.7
|
1.0
|
CZ
|
A:ARG72
|
4.6
|
27.7
|
0.5
|
O
|
A:SER40
|
4.7
|
20.8
|
1.0
|
C
|
A:SER40
|
4.7
|
21.8
|
1.0
|
C
|
A:GLU39
|
4.8
|
27.6
|
1.0
|
N
|
A:SER40
|
4.9
|
24.9
|
1.0
|
CD1
|
A:TYR42
|
4.9
|
15.1
|
1.0
|
NE
|
A:ARG72
|
4.9
|
25.0
|
0.5
|
|
Reference:
K.El Omari,
R.Duman,
V.Mykhaylyk,
C.M.Orr,
M.Latimer-Smith,
G.Winter,
V.Grama,
F.Qu,
K.Bountra,
H.S.Kwong,
M.Romano,
R.I.Reis,
L.Vogeley,
L.Vecchia,
C.D.Owen,
S.Wittmann,
M.Renner,
M.Senda,
N.Matsugaki,
Y.Kawano,
T.A.Bowden,
I.Moraes,
J.M.Grimes,
E.J.Mancini,
M.A.Walsh,
C.R.Guzzo,
R.J.Owens,
E.Y.Jones,
D.G.Brown,
D.I.Stuart,
K.Beis,
A.Wagner.
Experimental Phasing Opportunities For Macromolecular Crystallography at Very Long Wavelengths. Commun Chem V. 6 219 2023.
ISSN: ESSN 2399-3669
PubMed: 37828292
DOI: 10.1038/S42004-023-01014-0
Page generated: Tue Jul 30 11:41:32 2024
|