Zinc in PDB 2vql: Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III), PDB code: 2vql 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)	60.75 / 3.16
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.392, 78.392, 191.859, 90.00, 90.00, 90.00
R / Rfree (%)	28.1 / 30.7

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

Arsenic

(As)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III) (pdb code 2vql). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III), PDB code: 2vql:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1089 b:0.8 occ:1.00 O1 A:CAC1094 1.7 0.8 1.0 OE2 A:GLU37 2.0 0.2 1.0 O2 A:CAC1093 2.3 0.8 1.0 O1 A:CAC1093 2.5 0.8 1.0 AS A:CAC1093 2.9 0.8 1.0 CD A:GLU37 3.0 0.2 1.0 AS A:CAC1094 3.2 0.8 1.0 OE1 A:GLU37 3.4 0.8 1.0 O2 A:CAC1094 3.6 0.8 1.0 C2 A:CAC1093 4.1 0.8 1.0 ZN A:ZN1090 4.1 0.8 1.0 C2 A:CAC1094 4.2 0.8 1.0 CG A:GLU37 4.4 0.5 1.0 C1 A:CAC1093 4.5 0.8 1.0 C1 A:CAC1094 4.6 0.8 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1090 b:0.8 occ:1.00 O2 A:CAC1094 1.8 0.8 1.0 OE2 A:GLU26 1.9 98.0 1.0 O1 A:CAC1093 1.9 0.8 1.0 CD A:GLU26 3.0 96.4 1.0 AS A:CAC1094 3.1 0.8 1.0 AS A:CAC1093 3.1 0.8 1.0 C1 A:CAC1093 3.3 0.8 1.0 OE1 A:GLU26 3.5 97.4 1.0 C2 A:CAC1094 3.6 0.8 1.0 NZ A:LYS30 3.6 0.7 1.0 O1 A:CAC1094 3.9 0.8 1.0 ZN A:ZN1089 4.1 0.8 1.0 CG A:GLU26 4.3 94.0 1.0 C2 A:CAC1093 4.3 0.8 1.0 O2 A:CAC1093 4.4 0.8 1.0 CE A:LYS30 4.5 0.6 1.0 C1 A:CAC1094 4.7 0.8 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1091 b:0.8 occ:1.00 OD1 A:ASP76 2.6 92.5 1.0 OD2 A:ASP76 2.8 96.3 1.0 CG A:ASP76 3.1 93.5 1.0 OD1 B:ASP76 3.2 91.1 1.0 OD2 B:ASP76 3.8 93.6 1.0 CG B:ASP76 3.9 92.0 1.0 OD1 A:ASN41 4.2 90.4 1.0 OD1 B:ASN41 4.5 87.3 1.0 ND2 A:ASN41 4.5 92.1 1.0 O A:ALA72 4.5 86.4 1.0 CB A:ASP76 4.6 92.3 1.0 CG A:ASN41 4.6 91.5 1.0 CG B:ASN41 4.8 88.0 1.0 ND2 B:ASN41 4.9 88.6 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1092 b:0.8 occ:1.00 OE2 B:GLU46 2.0 95.3 1.0 OD2 A:ASP69 2.3 98.5 1.0 OD1 A:ASP65 2.4 98.3 1.0 OD1 A:ASP69 2.5 94.8 1.0 CD B:GLU46 2.7 93.4 1.0 OE1 B:GLU46 2.7 94.5 1.0 CG A:ASP69 2.8 94.9 1.0 OD2 A:ASP65 3.0 0.8 1.0 CG A:ASP65 3.0 98.5 1.0 NH1 B:ARG42 4.0 92.8 1.0 CG B:GLU46 4.2 90.3 1.0 CB A:ASP69 4.3 91.5 1.0 CB A:ASP65 4.5 96.5 1.0 CD B:ARG42 4.5 94.6 1.0 O A:ASP65 4.7 89.7 1.0 CG B:ARG42 4.9 93.0 1.0 C A:ASP65 5.0 90.8 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1089 b:0.8 occ:1.00 OE2 A:GLU68 2.0 92.9 1.0 OE1 B:GLU68 2.2 90.9 1.0 OE2 B:GLU68 2.2 89.9 1.0 OE1 A:GLU68 2.4 93.8 1.0 CD B:GLU68 2.5 89.2 1.0 CD A:GLU68 2.5 91.7 1.0 CG B:GLU68 4.0 87.2 1.0 CG A:GLU68 4.0 88.3 1.0 CB B:GLU68 4.9 87.2 1.0 CB A:GLU68 5.0 88.0 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1090 b:0.8 occ:1.00 OE2 A:GLU46 2.0 99.2 1.0 OD2 B:ASP69 2.1 96.1 1.0 OD2 B:ASP65 2.2 0.1 1.0 OD1 B:ASP65 2.5 95.7 1.0 CG B:ASP65 2.7 96.9 1.0 CD A:GLU46 2.8 96.8 1.0 CG B:ASP69 2.8 94.7 1.0 OD1 B:ASP69 2.8 95.5 1.0 OE1 A:GLU46 2.9 98.7 1.0 CB B:ASP65 4.1 95.1 1.0 CG A:GLU46 4.2 92.4 1.0 CB B:ASP69 4.3 92.7 1.0 O B:ASP65 4.4 90.3 1.0 C B:ASP65 4.5 91.3 1.0 CA B:ASP65 4.8 92.0 1.0 N B:TRP66 5.0 92.4 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1091 b:0.8 occ:1.00 O2 B:CAC1093 1.9 0.8 1.0 O2 B:CAC1094 2.1 0.8 1.0 OE2 B:GLU26 2.1 0.2 1.0 CD B:GLU26 2.8 0.2 1.0 OE1 B:GLU26 2.8 0.9 1.0 AS B:CAC1094 2.9 0.8 1.0 C2 B:CAC1094 3.2 0.8 1.0 AS B:CAC1093 3.3 0.8 1.0 O1 B:CAC1094 3.5 0.8 1.0 NZ B:LYS30 3.5 0.8 1.0 C2 B:CAC1093 3.8 0.8 1.0 CG B:GLU26 4.2 0.6 1.0 O1 B:CAC1093 4.3 0.8 1.0 ZN B:ZN1092 4.5 0.8 1.0 CE B:LYS30 4.7 0.5 1.0 C1 B:CAC1094 4.8 0.8 1.0 C1 B:CAC1093 4.8 0.8 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


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 III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1092 b:0.8 occ:1.00 O1 B:CAC1093 1.8 0.8 1.0 O1 B:CAC1094 2.0 0.8 1.0 OE2 B:GLU37 2.1 0.8 1.0 OE1 B:GLU37 2.7 0.6 1.0 CD B:GLU37 2.7 0.3 1.0 AS B:CAC1094 3.0 0.8 1.0 AS B:CAC1093 3.1 0.8 1.0 O2 B:CAC1094 3.4 0.8 1.0 C1 B:CAC1094 3.5 0.8 1.0 C2 B:CAC1093 3.7 0.8 1.0 O2 B:CAC1093 3.8 0.8 1.0 CG B:GLU37 4.2 0.3 1.0 ZN B:ZN1091 4.5 0.8 1.0 C1 B:CAC1093 4.8 0.8 1.0 C2 B:CAC1094 4.8 0.8 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1089 b:0.8 occ:1.00 OD2 C:ASP65 2.1 0.1 1.0 OD2 C:ASP69 2.1 0.4 1.0 CG C:ASP69 2.7 0.3 1.0 OD1 C:ASP69 2.8 0.8 1.0 CG C:ASP65 3.2 0.6 1.0 OD1 C:ASP65 3.7 0.2 1.0 O C:ASP65 4.0 0.7 1.0 CB C:ASP69 4.0 0.4 1.0 CB C:ASP65 4.4 0.4 1.0 C C:ASP65 4.7 0.4 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form III) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1090 b:0.8 occ:1.00 OE2 C:GLU68 2.6 0.5 1.0 OE1 C:GLU68 2.9 0.0 1.0 CD C:GLU68 3.1 0.3 1.0 CG C:GLU68 4.6 0.0 1.0

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