Zinc in PDB 2vqg: Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)

The structure of Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I), PDB code: 2vqg 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)	72.36 / 1.82
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.070, 87.070, 260.530, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.5

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

Arsenic

(As)

13 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I) (pdb code 2vqg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 42 binding sites of Zinc where determined in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I), PDB code: 2vqg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1089 b:11.1 occ:0.90 O2 A:CAC1092 1.7 64.8 0.9 O2 A:CAC1093 1.8 60.9 0.9 OE2 A:GLU26 1.9 15.6 1.0 OE2 F:GLU26 2.0 13.4 1.0 CD A:GLU26 2.8 13.4 1.0 CD F:GLU26 2.8 14.2 1.0 AS A:CAC1093 2.9 63.4 0.9 AS A:CAC1092 3.0 67.0 0.9 OE1 F:GLU26 3.0 14.8 1.0 OE1 A:GLU26 3.1 13.3 1.0 C1 A:CAC1093 3.3 61.7 0.9 O1 A:CAC1092 3.3 65.8 0.9 O1 A:CAC1093 3.5 60.9 0.9 NZ F:LYS30 3.7 12.2 1.0 NZ A:LYS30 3.8 13.6 1.0 C2 A:CAC1092 4.0 65.7 0.9 CG A:GLU26 4.2 14.9 1.0 CG F:GLU26 4.2 13.1 1.0 CE A:LYS30 4.3 15.3 1.0 CE F:LYS30 4.3 14.8 1.0 C2 A:CAC1093 4.6 62.0 0.9 C1 A:CAC1092 4.6 66.0 0.9 ZN A:ZN1090 4.7 54.3 0.9

Zinc binding site 2 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1090 b:54.3 occ:0.90 OE2 A:GLU37 2.2 41.2 1.0 OE1 F:GLU37 2.5 42.3 1.0 O1 A:CAC1092 2.7 65.8 0.9 O1 A:CAC1093 2.8 60.9 0.9 OE2 F:GLU37 2.8 41.9 1.0 OE1 A:GLU37 2.8 41.9 1.0 CD A:GLU37 2.9 39.6 1.0 CD F:GLU37 2.9 39.6 1.0 C1 A:CAC1093 3.0 61.7 0.9 C2 A:CAC1092 3.0 65.7 0.9 AS A:CAC1092 3.4 67.0 0.9 AS A:CAC1093 3.4 63.4 0.9 CG F:GLU37 4.3 35.5 1.0 CG A:GLU37 4.3 35.5 1.0 O2 A:CAC1092 4.6 64.8 0.9 C2 A:CAC1093 4.7 62.0 0.9 ZN A:ZN1089 4.7 11.1 0.9 O2 A:CAC1093 4.8 60.9 0.9 C1 A:CAC1092 4.9 66.0 0.9 O F:HOH2010 5.0 26.1 1.0 CA F:GLU37 5.0 32.3 1.0

Zinc binding site 3 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1091 b:36.4 occ:0.50 OD2 A:ASP69 2.0 25.7 1.0 OD2 A:ASP65 2.2 24.2 0.5 ZN A:ZN1095 2.4 36.7 0.5 CG A:ASP65 3.1 20.6 0.5 CG A:ASP69 3.2 23.4 1.0 OD1 A:ASP65 3.4 24.3 0.5 OD1 A:ASP69 3.8 26.1 1.0 O A:HOH2028 4.1 34.1 1.0 CB A:ASP69 4.4 21.0 1.0 CB A:ASP65 4.5 18.3 0.5 CB A:ASP65 4.5 17.4 0.5 O A:ASP65 4.7 17.8 1.0 C A:ASP65 4.9 17.6 1.0

Zinc binding site 4 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1094 b:37.4 occ:0.50 O1 A:CAC1096 2.0 43.4 0.5 OE1 A:GLU36 2.2 41.4 1.0 O1 A:CAC1097 2.3 38.4 0.5 OE2 A:GLU36 2.4 39.9 1.0 O A:HOH2044 2.4 45.8 1.0 CD A:GLU36 2.6 38.1 1.0 O2 A:CAC1097 2.8 39.0 0.5 AS A:CAC1097 3.0 39.3 0.5 AS A:CAC1096 3.2 43.3 0.5 ZN A:ZN1099 3.5 31.9 0.5 O2 A:CAC1096 3.6 43.2 0.5 ZN A:ZN1098 3.6 36.1 0.5 C1 A:CAC1096 3.8 43.5 0.5 CG A:GLU36 4.1 32.8 1.0 O A:HOH2046 4.1 40.9 1.0 C2 A:CAC1097 4.1 38.1 0.5 C1 A:CAC1097 4.7 38.7 0.5 O A:HOH2047 4.7 41.4 1.0 CB A:GLU36 4.8 29.8 1.0 C2 A:CAC1096 4.9 43.4 0.5

Zinc binding site 5 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1095 b:36.7 occ:0.50 OD1 A:ASP65 2.2 24.3 0.5 ZN A:ZN1091 2.4 36.4 0.5 OD2 A:ASP69 2.5 25.7 1.0 OD1 A:ASP69 2.6 26.1 1.0 CG A:ASP65 2.9 20.6 0.5 CG A:ASP69 2.9 23.4 1.0 OD2 A:ASP65 2.9 24.2 0.5 O A:ASP65 4.3 17.8 1.0 CB A:ASP65 4.3 18.3 0.5 CB A:ASP65 4.3 17.4 0.5 CB A:ASP69 4.4 21.0 1.0 CG A:ASP65 4.7 18.3 0.5 O A:HOH2036 4.8 38.1 1.0 C A:ASP65 4.8 17.6 1.0 CA A:ASP65 4.9 17.6 0.5 CA A:ASP65 4.9 18.0 0.5

Zinc binding site 6 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1098 b:36.1 occ:0.50 O2 A:CAC1096 1.8 43.2 0.5 ZN A:ZN1099 2.0 31.9 0.5 O1 A:CAC1097 2.0 38.4 0.5 O A:HOH2047 2.2 41.4 1.0 AS A:CAC1096 3.1 43.3 0.5 AS A:CAC1097 3.2 39.3 0.5 OE1 A:GLU36 3.2 41.4 1.0 O1 A:CAC1096 3.3 43.4 0.5 C1 A:CAC1097 3.4 38.7 0.5 ZN A:ZN1094 3.6 37.4 0.5 O2 A:CAC1097 4.2 39.0 0.5 C2 A:CAC1096 4.2 43.4 0.5 O A:HOH2011 4.3 33.0 1.0 CD A:GLU36 4.5 38.1 1.0 C1 A:CAC1096 4.6 43.5 0.5 O A:GLY33 4.7 19.6 1.0 C2 A:CAC1097 4.8 38.1 0.5

Zinc binding site 7 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1099 b:31.9 occ:0.50 O1 A:CAC1097 1.8 38.4 0.5 ZN A:ZN1098 2.0 36.1 0.5 O1 A:CAC1096 2.5 43.4 0.5 O2 A:CAC1096 2.8 43.2 0.5 AS A:CAC1096 2.9 43.3 0.5 AS A:CAC1097 3.4 39.3 0.5 C2 A:CAC1096 3.5 43.4 0.5 ZN A:ZN1094 3.5 37.4 0.5 O A:HOH2047 4.1 41.4 1.0 C1 A:CAC1097 4.2 38.7 0.5 C2 A:CAC1097 4.2 38.1 0.5 OE1 A:GLU36 4.2 41.4 1.0 O2 A:CAC1097 4.7 39.0 0.5 C1 A:CAC1096 4.8 43.5 0.5

Zinc binding site 8 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1088 b:10.2 occ:0.90 O2 B:CAC1093 1.9 18.1 0.9 OE2 B:GLU26 2.0 13.6 1.0 OE2 E:GLU26 2.0 13.5 1.0 O2 B:CAC1092 2.2 24.1 0.9 CD B:GLU26 2.8 11.3 1.0 CD E:GLU26 2.8 10.7 1.0 OE1 B:GLU26 2.9 11.5 1.0 OE1 E:GLU26 3.1 11.7 1.0 AS B:CAC1093 3.2 20.5 0.9 AS B:CAC1092 3.3 28.8 0.9 NZ B:LYS30 3.5 31.0 1.0 C2 B:CAC1092 3.6 29.8 0.9 NZ E:LYS30 3.6 20.0 1.0 C2 B:CAC1093 3.7 23.2 0.9 O1 B:CAC1092 3.9 29.5 0.9 O1 B:CAC1093 3.9 24.3 0.9 CG B:GLU26 4.2 11.6 1.0 CG E:GLU26 4.2 12.1 1.0 CE E:LYS30 4.3 21.3 1.0 CE B:LYS30 4.3 29.4 1.0 ZN B:ZN1089 4.5 21.4 0.9 C1 B:CAC1093 4.7 23.0 0.9 O E:HOH2009 4.9 13.8 1.0 O E:HOH2006 5.0 16.6 1.0 C1 B:CAC1092 5.0 30.7 0.9

Zinc binding site 9 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1089 b:21.4 occ:0.90 O1 B:CAC1092 1.7 29.5 0.9 O1 B:CAC1093 1.8 24.3 0.9 OE1 B:GLU37 2.2 36.6 1.0 OE1 E:GLU37 2.3 31.4 1.0 OE2 B:GLU37 2.4 35.8 1.0 OE2 E:GLU37 2.4 33.1 1.0 CD B:GLU37 2.6 34.1 1.0 CD E:GLU37 2.7 28.1 1.0 AS B:CAC1092 3.2 28.8 0.9 AS B:CAC1093 3.3 20.5 0.9 O E:HOH2019 3.7 30.6 1.0 O2 B:CAC1093 3.7 18.1 0.9 O2 B:CAC1092 3.8 24.1 0.9 O B:HOH2014 3.8 36.0 1.0 CG B:GLU37 4.1 29.7 1.0 CG E:GLU37 4.2 25.9 1.0 C1 B:CAC1093 4.2 23.0 0.9 C1 B:CAC1092 4.4 30.7 0.9 ZN B:ZN1088 4.5 10.2 0.9 C2 B:CAC1092 4.6 29.8 0.9 C2 B:CAC1093 4.8 23.2 0.9 CB E:GLU37 5.0 23.2 1.0

Zinc binding site 10 out of 42 in the Crystal Structure of Porb From Corynebacterium Glutamicum ( Crystal Form I)


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 I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1090 b:34.3 occ:0.50 OD1 B:ASP65 2.2 9.6 0.5 OD1 B:ASP69 2.2 17.0 1.0 ZN B:ZN1095 2.5 30.8 0.5 CG B:ASP69 2.9 17.7 1.0 OD2 B:ASP69 3.0 19.1 1.0 CG B:ASP65 3.0 11.1 0.5 O B:HOH2050 3.0 16.6 0.5 OD2 B:ASP65 3.2 10.9 0.5 O B:ASP65 4.2 13.7 0.5 O B:ASP65 4.3 12.8 0.5 CB B:ASP69 4.4 15.7 1.0 CB B:ASP65 4.4 12.1 0.5 CB B:ASP65 4.4 14.9 0.5 CG B:ASP65 4.6 18.2 0.5 C B:ASP65 4.8 14.2 0.5 C B:ASP65 4.8 13.2 0.5 CA B:ASP65 4.8 14.5 0.5 CA B:ASP65 4.9 12.8 0.5 OD1 B:ASP65 4.9 22.1 0.5 CA B:ASP69 5.0 16.1 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