Zinc in PDB 2y8b: 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: 2y8b 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)	28.00 / 1.70
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	69.758, 69.758, 46.942, 90.00, 90.00, 90.00
R / Rfree (%)	17.115 / 21.472

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 2y8b). 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: 2y8b:
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:13.3 occ:1.00 O A:HOH2188 2.0 11.7 1.0 ND1 A:HIS118 2.0 10.1 1.0 NE2 A:HIS196 2.0 9.6 1.0 NE2 A:HIS116 2.1 7.6 1.0 O A:HOH2187 2.6 21.2 1.0 CE1 A:HIS118 3.0 11.6 1.0 CD2 A:HIS196 3.0 11.1 1.0 CG A:HIS118 3.0 11.2 1.0 CE1 A:HIS196 3.0 14.8 1.0 CE1 A:HIS116 3.1 7.2 1.0 CD2 A:HIS116 3.1 6.0 1.0 CB A:HIS118 3.4 9.1 1.0 OD2 A:OCS221 3.5 10.9 0.5 ZN A:ZN1293 3.6 16.8 0.5 OD1 A:ASP120 4.0 12.0 1.0 NE2 A:HIS118 4.1 13.0 1.0 ND1 A:HIS196 4.1 9.4 1.0 CD2 A:HIS118 4.1 13.2 1.0 CG A:HIS196 4.1 8.2 1.0 ND1 A:HIS116 4.2 7.0 1.0 CG A:HIS116 4.2 7.7 1.0 SG A:OCS221 4.4 17.5 1.0 O A:HOH2042 4.5 33.0 1.0 OD1 A:OCS221 4.5 6.7 1.0 CB A:OCS221 4.5 11.0 1.0 OD2 A:ASP120 4.7 13.1 1.0 CG A:ASP120 4.8 12.5 1.0 CA A:HIS118 4.8 8.5 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:16.8 occ:0.50 OD2 A:OCS221 1.2 10.9 0.5 SG A:OCS221 2.0 17.5 1.0 O A:HOH2188 2.1 11.7 1.0 NE2 A:HIS263 2.3 18.4 1.0 OD2 A:ASP120 2.3 13.1 1.0 OD1 A:OCS221 2.4 6.7 1.0 OD3 A:OCS221 2.8 13.7 0.5 CD2 A:HIS263 3.1 21.5 1.0 CG A:ASP120 3.3 12.5 1.0 CE1 A:HIS263 3.4 18.7 1.0 CB A:OCS221 3.5 11.0 1.0 OD1 A:ASP120 3.6 12.0 1.0 ZN A:ZN1292 3.6 13.3 1.0 NH2 A:ARG121 3.9 13.9 1.0 CE1 A:HIS116 4.1 7.2 1.0 O A:HOH2187 4.2 21.2 1.0 NE A:ARG121 4.2 7.5 1.0 NE2 A:HIS196 4.3 9.6 1.0 CG A:HIS263 4.3 14.7 1.0 NE2 A:HIS116 4.4 7.6 1.0 ND1 A:HIS263 4.4 20.1 1.0 CZ A:ARG121 4.5 11.1 1.0 CE1 A:HIS196 4.6 14.8 1.0 CB A:ASP120 4.6 9.0 1.0 CA A:OCS221 4.7 10.9 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