Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg1295 b:13.9 occ:1.00 O A:HOH2066 1.8 28.3 1.0 O A:HOH2097 2.0 24.3 1.0 O A:HOH2095 2.3 38.8 1.0 OD1 A:ASN165 2.4 13.5 1.0 OD2 A:ASP119 2.5 20.6 1.0 OD1 A:ASP119 2.6 15.7 1.0 O A:HOH2093 2.7 37.0 1.0 CG A:ASP119 2.9 14.6 1.0 CG A:ASN165 3.4 13.8 1.0 ND2 A:ASN165 4.1 11.3 1.0 O A:HOH2099 4.4 19.0 1.0 CB A:ASP119 4.4 8.2 1.0 CB A:ASN165 4.5 9.6 1.0 CA A:ASN165 4.6 11.1 1.0 O A:HOH2067 4.7 13.9 1.0 O A:GLY150 4.7 14.6 1.0 O A:HOH2101 4.9 30.2 1.0 O A:ALA149 4.9 13.9 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