Zinc in PDB 6op7: Structure of Oxidized Vim-20

The structure of Structure of Oxidized Vim-20, PDB code: 6op7 was solved by R.C.Page, B.A.Shurina, J.S.Montgomery, M.G.Orischak, J.C.Nix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.68 / 1.37
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.860, 77.860, 79.360, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.2

The binding sites of Zinc atom in the Structure of Oxidized Vim-20 (pdb code 6op7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Oxidized Vim-20, PDB code: 6op7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Oxidized Vim-20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Oxidized Vim-20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.6 occ:1.00 O A:HOH408 1.9 17.0 1.0 ND1 A:HIS116 2.0 15.1 1.0 NE2 A:HIS179 2.0 13.1 1.0 NE2 A:HIS114 2.1 13.7 1.0 O A:HOH497 2.3 21.7 1.0 CE1 A:HIS116 3.0 17.4 1.0 CD2 A:HIS179 3.0 13.3 1.0 CG A:HIS116 3.0 15.6 1.0 CE1 A:HIS179 3.0 13.5 1.0 CE1 A:HIS114 3.0 13.1 1.0 CD2 A:HIS114 3.2 12.4 1.0 CB A:HIS116 3.4 15.5 1.0 OD3 A:OCS198 3.7 16.5 1.0 OD1 A:ASP118 4.0 20.4 1.0 NE2 A:HIS116 4.1 17.9 1.0 ND1 A:HIS179 4.1 13.8 1.0 CD2 A:HIS116 4.1 17.8 1.0 CG A:HIS179 4.1 12.7 1.0 ND1 A:HIS114 4.2 12.4 1.0 CG A:HIS114 4.3 11.9 1.0 OD1 A:OCS198 4.5 15.2 1.0 SG A:OCS198 4.5 14.8 1.0 CB A:OCS198 4.6 13.4 1.0 CA A:HIS116 4.8 14.9 1.0 CG A:ASP118 4.8 20.0 1.0 OD2 A:ASP118 4.8 24.6 1.0 O A:HOH467 5.0 21.6 1.0

Zinc binding site 2 out of 2 in the Structure of Oxidized Vim-20


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Oxidized Vim-20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.0 occ:1.00 ND1 A:HIS251 2.1 16.1 1.0 CE1 A:HIS251 3.0 17.5 1.0 CG A:HIS251 3.1 15.2 1.0 CB A:HIS251 3.5 13.8 1.0 CA A:HIS251 3.8 13.8 1.0 NE2 A:HIS251 4.2 16.2 1.0 CD2 A:HIS251 4.2 15.8 1.0 ND2 A:ASN254 4.3 16.5 1.0 CD2 A:LEU203 4.4 16.5 1.0 O A:HIS251 4.7 14.4 1.0 C A:HIS251 4.7 14.2 1.0 N A:HIS251 4.8 14.7 1.0

Z.Cheng, B.A.Shurina, C.R.Bethel, P.W.Thomas, S.H.Marshall, C.A.Thomas, K.Yang, R.L.Kimble, J.S.Montgomery, M.G.Orischak, C.M.Miller, J.L.Tennenbaum, J.C.Nix, D.L.Tierney, W.Fast, R.A.Bonomo, R.C.Page, M.W.Crowder. A Single Salt Bridge in Vim-20 Increases Protein Stability and Antibiotic Resistance Under Low-Zinc Conditions. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 31744917
DOI: 10.1128/MBIO.02412-19