Zinc in PDB 6op6: Structure of Vim-20 in the Reduced State

The structure of Structure of Vim-20 in the Reduced State, PDB code: 6op6 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)	39.35 / 1.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.460, 74.256, 78.693, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.9

The structure of Structure of Vim-20 in the Reduced State also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Structure of Vim-20 in the Reduced State (pdb code 6op6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Vim-20 in the Reduced State, PDB code: 6op6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Vim-20 in the Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vim-20 in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.7 occ:1.00 O A:HOH527 2.0 24.6 1.0 NE2 A:HIS179 2.0 13.5 1.0 ND1 A:HIS116 2.0 19.6 1.0 NE2 A:HIS114 2.1 14.7 1.0 CE1 A:HIS114 3.0 13.5 1.0 CE1 A:HIS116 3.0 17.9 1.0 CD2 A:HIS179 3.0 12.8 1.0 CE1 A:HIS179 3.0 13.1 1.0 CG A:HIS116 3.0 15.2 1.0 CD2 A:HIS114 3.1 13.4 1.0 CB A:HIS116 3.4 15.1 1.0 ZN A:ZN302 3.6 25.8 1.0 OD1 A:ASP118 3.9 21.7 1.0 O A:HOH517 4.0 31.1 1.0 ND1 A:HIS114 4.1 13.5 1.0 ND1 A:HIS179 4.1 13.8 1.0 NE2 A:HIS116 4.1 21.0 1.0 CG A:HIS179 4.1 15.0 1.0 CD2 A:HIS116 4.1 16.2 1.0 CG A:HIS114 4.2 12.6 1.0 CB A:CYS198 4.2 14.6 1.0 SG A:CYS198 4.3 19.9 1.0 OD2 A:ASP118 4.5 19.3 1.0 CG A:ASP118 4.6 20.0 1.0 CA A:HIS116 4.8 15.8 1.0 ND2 A:ASN210 4.9 69.0 1.0 O A:HOH512 5.0 20.2 1.0

Zinc binding site 2 out of 3 in the Structure of Vim-20 in the Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vim-20 in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:25.8 occ:1.00 O A:HOH527 2.0 24.6 1.0 OD2 A:ASP118 2.1 19.3 1.0 NE2 A:HIS240 2.1 17.5 1.0 O A:HOH517 2.2 31.1 1.0 SG A:CYS198 2.3 19.9 1.0 CE1 A:HIS240 3.1 18.7 1.0 CD2 A:HIS240 3.1 16.0 1.0 CG A:ASP118 3.1 20.0 1.0 CB A:CYS198 3.4 14.6 1.0 O A:HOH580 3.5 44.4 1.0 OD1 A:ASP118 3.5 21.7 1.0 ZN A:ZN301 3.6 17.7 1.0 NH2 A:ARG119 3.8 24.3 1.0 NE A:ARG119 4.1 14.7 1.0 ND1 A:HIS240 4.2 17.2 1.0 CG A:HIS240 4.3 17.3 1.0 CE1 A:HIS114 4.3 13.5 1.0 NE2 A:HIS179 4.4 13.5 1.0 CB A:ASP118 4.4 15.2 1.0 O A:HOH583 4.4 30.3 1.0 CZ A:ARG119 4.4 15.5 1.0 O A:HOH513 4.5 24.2 1.0 CE1 A:HIS179 4.5 13.1 1.0 NE2 A:HIS114 4.5 14.7 1.0 CA A:CYS198 4.7 14.4 1.0

Zinc binding site 3 out of 3 in the Structure of Vim-20 in the Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vim-20 in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:15.5 occ:1.00 OE2 A:GLU266 2.0 20.7 1.0 ND1 A:HIS251 2.0 14.8 1.0 O A:HOH574 2.2 7.8 1.0 CD A:GLU266 2.9 54.0 1.0 CE1 A:HIS251 2.9 16.9 1.0 OE1 A:GLU266 3.0 24.0 1.0 CG A:HIS251 3.1 15.1 1.0 CB A:HIS251 3.6 17.4 1.0 CA A:HIS251 4.0 16.0 1.0 NE2 A:HIS251 4.1 14.7 1.0 CD2 A:HIS251 4.2 13.7 1.0 O A:HOH501 4.2 22.2 1.0 CG A:GLU266 4.3 23.9 1.0 O A:HIS251 4.6 15.6 1.0 C A:HIS251 4.7 14.6 1.0 O A:LEU203 4.8 17.1 1.0 O A:HOH429 4.9 49.0 1.0 ND2 A:ASN254 5.0 18.1 1.0 CD2 A:LEU203 5.0 18.9 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