Zinc in PDB 2y8a: Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases

The structure of Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases, PDB code: 2y8a was solved by P.Saradhi, H.-K.S.Leiros, R.Ahmad, J.Spencer, I.Leiros, T.R.Walsh, A.Sundsfjord, O.Samuelsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.33
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	70.138, 70.138, 47.529, 90.00, 90.00, 90.00
R / Rfree (%)	18.673 / 25.405

The structure of Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases (pdb code 2y8a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases, PDB code: 2y8a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1292 b:16.8 occ:1.00 NE2 A:HIS196 2.0 19.6 1.0 ND1 A:HIS118 2.1 17.5 1.0 NE2 A:HIS116 2.1 15.9 1.0 UNK A:UNX1295 2.3 23.2 1.0 CD2 A:HIS196 3.0 20.2 1.0 CE1 A:HIS118 3.0 17.4 1.0 CE1 A:HIS196 3.0 20.2 1.0 CG A:HIS118 3.1 18.5 1.0 CD2 A:HIS116 3.1 14.7 1.0 CE1 A:HIS116 3.1 17.9 1.0 CB A:HIS118 3.4 18.0 1.0 ZN A:ZN1293 3.8 20.6 1.0 ND1 A:HIS196 4.1 20.4 1.0 CG A:HIS196 4.1 20.3 1.0 O A:HOH2035 4.1 23.7 1.0 NE2 A:HIS118 4.1 17.4 1.0 ND1 A:HIS116 4.2 16.8 1.0 CD2 A:HIS118 4.2 18.5 1.0 CG A:HIS116 4.2 15.9 1.0 OD1 A:ASP120 4.2 16.3 1.0 CB A:CYS221 4.2 18.9 1.0 SG A:CYS221 4.4 20.2 1.0 OD2 A:ASP120 4.8 19.4 1.0 CA A:HIS118 4.8 18.0 1.0 CG A:ASP120 5.0 18.4 1.0

Zinc binding site 2 out of 2 in the Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-7 with Oxidised. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:20.6 occ:1.00 OD2 A:ASP120 2.0 19.4 1.0 NE2 A:HIS263 2.1 20.3 1.0 SG A:CYS221 2.2 20.2 1.0 UNK A:UNX1295 2.3 23.2 1.0 CD2 A:HIS263 3.1 21.2 1.0 CE1 A:HIS263 3.1 21.5 1.0 CG A:ASP120 3.1 18.4 1.0 OD1 A:ASP120 3.5 16.3 1.0 CB A:CYS221 3.5 18.9 1.0 O A:HOH2035 3.7 23.7 1.0 NH2 A:ARG121 3.7 23.2 1.0 ZN A:ZN1292 3.8 16.8 1.0 ND1 A:HIS263 4.2 21.6 1.0 NE A:ARG121 4.2 20.0 1.0 CG A:HIS263 4.2 21.3 1.0 CE1 A:HIS116 4.3 17.9 1.0 CB A:ASP120 4.4 17.8 1.0 CZ A:ARG121 4.4 21.6 1.0 NE2 A:HIS116 4.5 15.9 1.0 NE2 A:HIS196 4.7 19.6 1.0 CA A:CYS221 4.7 18.6 1.0 CE1 A:HIS196 4.8 20.2 1.0 O A:HOH2054 5.0 33.7 1.0

P.Saradhi, H.-K.S.Leiros, R.Ahmad, J.Spencer, I.Leiros, T.R.Walsh, A.Sundsfjord, O.Samuelsen. Structural and Computational Investigations of Vim- 7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases J.Mol.Biol. V. 411 174 2011.
ISSN: ISSN 0022-2836
PubMed: 21645522
DOI: 10.1016/J.JMB.2011.05.035