Zinc in PDB 2y87: Native Vim-7. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases

The structure of Native Vim-7. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases, PDB code: 2y87 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)	20.00 / 1.86
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	70.399, 70.399, 47.562, 90.00, 90.00, 90.00
R / Rfree (%)	16.023 / 21.011

The structure of Native Vim-7. 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 Native Vim-7. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases (pdb code 2y87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Native Vim-7. Structural and Computational Investigations of Vim-7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases, PDB code: 2y87:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Native Vim-7. 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 Native Vim-7. 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:10.3 occ:1.00 ND1 A:HIS118 2.0 6.8 1.0 O A:HOH2000 2.1 5.7 0.7 NE2 A:HIS116 2.1 5.6 1.0 NE2 A:HIS196 2.1 10.8 1.0 UNK A:UNX1296 2.5 14.9 0.3 CE1 A:HIS118 3.0 10.5 1.0 CD2 A:HIS116 3.0 5.8 1.0 CE1 A:HIS116 3.0 8.6 1.0 CG A:HIS118 3.0 8.7 1.0 CD2 A:HIS196 3.1 5.7 1.0 CE1 A:HIS196 3.1 13.1 1.0 CB A:HIS118 3.4 7.8 1.0 ZN A:ZN1294 3.7 13.0 1.0 OD1 A:ASP120 4.0 9.2 1.0 NE2 A:HIS118 4.1 11.4 1.0 ND1 A:HIS116 4.1 5.5 1.0 CD2 A:HIS118 4.2 9.6 1.0 CG A:HIS116 4.2 6.0 1.0 ND1 A:HIS196 4.2 8.8 1.0 CG A:HIS196 4.2 9.5 1.0 CB A:CYS221 4.3 8.3 1.0 SG A:CYS221 4.4 9.7 1.0 OD2 A:ASP120 4.6 7.8 1.0 CG A:ASP120 4.8 11.0 1.0 CA A:HIS118 4.8 7.6 1.0 O A:HOH2001 5.0 33.8 1.0

Zinc binding site 2 out of 2 in the Native Vim-7. 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 Native Vim-7. 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:Zn1294 b:13.0 occ:1.00 OD2 A:ASP120 2.0 7.8 1.0 NE2 A:HIS263 2.1 7.7 1.0 O A:HOH2000 2.3 5.7 0.7 SG A:CYS221 2.3 9.7 1.0 UNK A:UNX1296 2.4 14.9 0.3 CD2 A:HIS263 3.0 9.8 1.0 CG A:ASP120 3.1 11.0 1.0 CE1 A:HIS263 3.2 9.6 1.0 CB A:CYS221 3.4 8.3 1.0 OD1 A:ASP120 3.4 9.2 1.0 ZN A:ZN1293 3.7 10.3 1.0 NH2 A:ARG121 3.7 13.3 1.0 O A:HOH2001 3.9 33.8 1.0 NE A:ARG121 4.2 7.1 1.0 CE1 A:HIS116 4.2 8.6 1.0 CG A:HIS263 4.2 9.4 1.0 ND1 A:HIS263 4.2 8.5 1.0 NE2 A:HIS116 4.4 5.6 1.0 CZ A:ARG121 4.4 12.1 1.0 CB A:ASP120 4.4 8.6 1.0 NE2 A:HIS196 4.6 10.8 1.0 CA A:CYS221 4.7 9.3 1.0 O A:HOH2123 4.8 26.1 1.0 CE1 A:HIS196 4.9 13.1 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