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Arsenic in PDB 2vqk: Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV)

Protein crystallography data

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV), PDB code: 2vqk was solved by K.Ziegler, R.Benz, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.705 / 4.2
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.370, 81.370, 80.140, 90.00, 90.00, 120.00
R / Rfree (%) 41.86 / n/a

Other elements in 2vqk:

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV) also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV) (pdb code 2vqk). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV), PDB code: 2vqk:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 2vqk

Go back to Arsenic Binding Sites List in 2vqk
Arsenic binding site 1 out of 3 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1090

b:0.2
occ:0.50
AS A:CAC1090 0.0 0.2 0.5
O1 A:CAC1090 1.7 0.2 0.5
O2 A:CAC1090 1.7 0.2 0.5
C1 A:CAC1090 2.0 0.2 0.5
C2 A:CAC1090 2.0 0.2 0.5
ZN A:ZN1093 3.5 0.5 1.0
O2 A:CAC1092 4.0 0.2 0.5
O1 A:CAC1092 4.1 0.2 0.5
OD1 A:ASP76 4.3 0.5 1.0
AS A:CAC1092 4.8 0.2 0.5
OE1 A:GLN79 4.8 0.4 1.0
CG A:ASP76 4.9 0.9 1.0
ND2 A:ASN41 4.9 0.4 1.0

Arsenic binding site 2 out of 3 in 2vqk

Go back to Arsenic Binding Sites List in 2vqk
Arsenic binding site 2 out of 3 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1091

b:0.2
occ:1.00
AS A:CAC1091 0.0 0.2 1.0
O1 A:CAC1091 1.7 0.2 1.0
O2 A:CAC1091 1.7 0.2 1.0
C2 A:CAC1091 2.0 0.2 1.0
C1 A:CAC1091 2.0 0.2 1.0
ZN A:ZN1095 3.0 0.5 0.5
ZN A:ZN1094 3.3 0.5 0.5
OE1 A:GLU37 4.2 0.0 1.0
OE2 A:GLU37 4.4 0.9 1.0
OE2 A:GLU26 4.4 0.4 1.0
CD A:GLU37 4.7 0.4 1.0

Arsenic binding site 3 out of 3 in 2vqk

Go back to Arsenic Binding Sites List in 2vqk
Arsenic binding site 3 out of 3 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1092

b:0.2
occ:0.50
AS A:CAC1092 0.0 0.2 0.5
O2 A:CAC1092 1.7 0.2 0.5
O1 A:CAC1092 1.7 0.2 0.5
C2 A:CAC1092 2.0 0.2 0.5
C1 A:CAC1092 2.0 0.2 0.5
ZN A:ZN1093 3.5 0.5 1.0
O1 A:CAC1090 3.9 0.2 0.5
OD1 A:ASP76 4.1 0.5 1.0
O2 A:CAC1090 4.2 0.2 0.5
OD1 A:ASN41 4.4 0.3 1.0
OD2 A:ASP76 4.6 0.6 1.0
OD2 A:ASP87 4.7 0.0 1.0
CB A:ALA72 4.7 0.3 1.0
CG A:ASP76 4.8 0.9 1.0
AS A:CAC1090 4.8 0.2 0.5
CG A:ASN41 5.0 0.2 1.0

Reference:

K.Ziegler, R.Benz, G.E.Schulz. A Putative Alpha-Helical Porin From Corynebacterium Glutamicum. J.Mol.Biol. V. 379 482 2008.
ISSN: ISSN 0022-2836
PubMed: 18462756
DOI: 10.1016/J.JMB.2008.04.017
Page generated: Tue Oct 27 16:49:26 2020

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