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Zinc in PDB 2vqh: Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)

Protein crystallography data

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II), PDB code: 2vqh 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) 70.53 / 2.89
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 81.457, 81.457, 163.346, 90.00, 90.00, 120.00
R / Rfree (%) 24.7 / 25.6

Other elements in 2vqh:

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

Arsenic (As) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) (pdb code 2vqh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II), PDB code: 2vqh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2vqh

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Zinc binding site 1 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1089

b:0.4
occ:1.00
OE2 B:GLU68 2.1 74.2 1.0
OE2 A:GLU68 2.2 74.6 1.0
CD B:GLU68 2.9 71.0 1.0
CD A:GLU68 2.9 70.8 1.0
OE1 B:GLU68 2.9 75.2 1.0
OE1 A:GLU68 3.1 75.0 1.0
CG A:GLU68 4.2 67.1 1.0
CG B:GLU68 4.3 67.5 1.0
ZN B:ZN1091 4.4 0.6 1.0

Zinc binding site 2 out of 8 in 2vqh

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Zinc binding site 2 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1090

b:91.5
occ:1.00
OD2 A:ASP69 1.8 79.1 1.0
OE2 B:GLU46 2.0 77.6 1.0
OD1 A:ASP65 2.3 74.0 1.0
OE1 B:GLU46 2.6 76.8 1.0
CD B:GLU46 2.6 73.7 1.0
OD2 A:ASP65 2.7 83.0 1.0
CG A:ASP69 2.8 73.4 1.0
CG A:ASP65 2.9 77.3 1.0
OD1 A:ASP69 3.1 74.9 1.0
CG B:GLU46 4.0 66.4 1.0
CB A:ASP69 4.2 68.8 1.0
CB A:ASP65 4.4 77.0 1.0
O A:ASP65 4.5 67.5 1.0
NE B:ARG42 4.5 73.6 1.0
CD B:ARG42 4.5 73.6 1.0
C A:ASP65 4.8 70.4 1.0
CB B:GLU46 4.9 64.0 1.0

Zinc binding site 3 out of 8 in 2vqh

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Zinc binding site 3 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1091

b:83.7
occ:1.00
OD2 A:ASP76 1.8 70.8 1.0
OD2 B:ASP87 2.6 80.0 1.0
CG A:ASP76 2.8 67.3 1.0
O1 B:CAC1092 2.8 91.1 1.0
C2 B:CAC1092 2.9 92.2 1.0
AS B:CAC1092 3.0 91.9 1.0
OD1 A:ASP76 3.1 66.8 1.0
O2 B:CAC1092 3.1 92.8 1.0
CB B:ASP87 3.2 86.8 1.0
CG B:ASP87 3.3 80.9 1.0
CB A:ASP76 4.2 65.2 1.0
OD1 B:ASP87 4.5 80.8 1.0
O A:ALA72 4.6 55.9 1.0
CA B:ASP87 4.7 89.5 1.0
C1 B:CAC1092 4.9 92.3 1.0

Zinc binding site 4 out of 8 in 2vqh

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Zinc binding site 4 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1092

b:70.3
occ:1.00
O2 A:CAC1095 1.8 76.6 1.0
OE2 A:GLU26 1.8 67.4 1.0
O2 A:CAC1094 1.9 77.8 1.0
CD A:GLU26 2.9 66.1 1.0
AS A:CAC1095 3.1 76.2 1.0
AS A:CAC1094 3.1 78.6 1.0
OE1 A:GLU26 3.4 68.7 1.0
O1 A:CAC1094 3.6 78.6 1.0
C2 A:CAC1095 3.6 75.8 1.0
NZ A:LYS30 3.6 70.0 1.0
C2 A:CAC1094 3.8 77.3 1.0
O1 A:CAC1095 3.8 77.7 1.0
CE A:LYS30 4.1 67.2 1.0
ZN A:ZN1093 4.1 80.6 1.0
CG A:GLU26 4.2 62.9 1.0
C1 A:CAC1095 4.7 75.6 1.0
C1 A:CAC1094 4.8 77.6 1.0

Zinc binding site 5 out of 8 in 2vqh

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Zinc binding site 5 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1093

b:80.6
occ:1.00
O1 A:CAC1095 1.7 77.7 1.0
O1 A:CAC1094 1.7 78.6 1.0
OE2 A:GLU37 2.0 85.2 1.0
CD A:GLU37 2.8 84.5 1.0
OE1 A:GLU37 2.9 84.1 1.0
AS A:CAC1094 3.1 78.6 1.0
AS A:CAC1095 3.2 76.2 1.0
C2 A:CAC1094 3.5 77.3 1.0
O2 A:CAC1095 3.8 76.6 1.0
C2 A:CAC1095 3.9 75.8 1.0
O2 A:CAC1094 4.1 77.8 1.0
ZN A:ZN1092 4.1 70.3 1.0
CG A:GLU37 4.2 83.7 1.0
C1 A:CAC1094 4.6 77.6 1.0
C1 A:CAC1095 4.7 75.6 1.0

Zinc binding site 6 out of 8 in 2vqh

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Zinc binding site 6 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1089

b:73.0
occ:1.00
OE2 A:GLU46 1.8 71.8 1.0
OD2 B:ASP69 2.2 79.3 1.0
OD1 B:ASP69 2.5 75.6 1.0
OD1 B:ASP65 2.5 84.4 1.0
CG B:ASP69 2.6 74.4 1.0
CD A:GLU46 2.8 67.5 1.0
OE1 A:GLU46 3.1 68.6 1.0
CG B:ASP65 3.2 82.4 1.0
OD2 B:ASP65 3.2 85.2 1.0
CB B:ASP69 4.1 70.4 1.0
CG A:GLU46 4.2 64.3 1.0
O B:ASP65 4.4 70.7 1.0
CB B:ASP65 4.6 79.9 1.0
CG A:ARG42 4.7 64.0 1.0
C B:ASP65 4.9 73.0 1.0
NE A:ARG42 4.9 62.6 1.0
CA B:ASP69 5.0 66.9 1.0

Zinc binding site 7 out of 8 in 2vqh

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Zinc binding site 7 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1090

b:97.9
occ:1.00
O1 B:CAC1092 2.3 91.1 1.0
OD1 B:ASP76 2.3 72.9 1.0
OD2 B:ASP76 2.5 77.2 1.0
CG B:ASP76 2.8 73.1 1.0
C1 B:CAC1092 3.0 92.3 1.0
AS B:CAC1092 3.2 91.9 1.0
OD2 A:ASP87 3.6 85.6 1.0
O B:ALA72 3.8 62.2 1.0
OD1 B:ASN41 4.1 66.0 1.0
CB B:ASP76 4.3 70.4 1.0
O2 B:CAC1092 4.4 92.8 1.0
C B:ALA72 4.5 61.4 1.0
CB B:ALA72 4.6 63.5 1.0
ND2 B:ASN41 4.6 66.7 1.0
C2 B:CAC1092 4.6 92.2 1.0
CG A:ASP87 4.6 84.3 1.0
CG B:ASN41 4.7 67.4 1.0
CA B:ALA72 4.8 60.5 1.0

Zinc binding site 8 out of 8 in 2vqh

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Zinc binding site 8 out of 8 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1091

b:0.6
occ:1.00
OE1 B:GLU53 2.8 80.8 1.0
OE2 B:GLU53 2.9 87.8 1.0
CD B:GLU53 3.1 82.5 1.0
OE2 B:GLU68 4.3 74.2 1.0
ZN A:ZN1089 4.4 0.4 1.0
CG B:GLU53 4.5 82.2 1.0
OE1 A:GLU68 4.8 75.0 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: Thu Oct 29 08:16:03 2020
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