Zinc in PDB 9cv3: Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril, PDB code: 9cv3 was solved by S.B.Silwal, J.C.Nix, R.C.Page, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.80 / 1.51
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.845, 77.595, 79.052, 90, 90, 90
R / Rfree (%)	19.2 / 21.2

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril (pdb code 9cv3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril, PDB code: 9cv3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.7 occ:1.00 NE2 A:HIS179 2.1 7.5 1.0 NE2 A:HIS114 2.1 9.1 1.0 ND1 A:HIS116 2.2 11.2 1.0 S A:X8Z304 2.2 10.5 0.8 CE1 A:HIS179 3.0 9.9 1.0 CD2 A:HIS179 3.0 8.0 1.0 C1 A:X8Z304 3.1 12.1 0.8 CE1 A:HIS114 3.1 9.6 1.0 CG A:HIS116 3.1 10.7 1.0 CD2 A:HIS114 3.1 9.3 1.0 CE1 A:HIS116 3.1 11.7 1.0 CB A:HIS116 3.4 10.4 1.0 ZN A:ZN302 3.7 12.5 1.0 CB A:CYS198 4.0 10.2 1.0 OD1 A:ASP118 4.1 12.6 1.0 ND1 A:HIS179 4.1 9.2 1.0 CG A:HIS179 4.2 8.2 1.0 ND1 A:HIS114 4.2 8.3 1.0 NE2 A:HIS116 4.2 10.5 1.0 CG A:HIS114 4.2 8.3 1.0 SG A:CYS198 4.2 11.2 1.0 CD2 A:HIS116 4.2 11.3 1.0 C2 A:X8Z304 4.5 11.8 0.8 OD2 A:ASP118 4.6 12.4 1.0 O1 A:X8Z304 4.8 13.6 0.8 CG A:ASP118 4.8 13.1 1.0 O A:HOH530 4.8 21.4 1.0 CA A:HIS116 4.8 9.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.5 occ:1.00 OD2 A:ASP118 1.9 12.4 1.0 NE2 A:HIS240 2.1 10.9 1.0 SG A:CYS198 2.3 11.2 1.0 S A:X8Z304 2.3 10.5 0.8 CG A:ASP118 3.0 13.1 1.0 CE1 A:HIS240 3.1 10.2 1.0 CD2 A:HIS240 3.1 12.3 1.0 C1 A:X8Z304 3.3 12.1 0.8 CB A:CYS198 3.4 10.2 1.0 OD1 A:ASP118 3.5 12.6 1.0 NH2 A:ARG119 3.6 12.7 1.0 ZN A:ZN301 3.7 10.7 1.0 C2 A:X8Z304 3.8 11.8 0.8 NE A:ARG119 4.0 9.4 1.0 ND1 A:HIS240 4.2 12.0 1.0 CG A:HIS240 4.2 11.9 1.0 CZ A:ARG119 4.3 10.9 1.0 CB A:ASP118 4.3 11.5 1.0 CH3 A:ACT307 4.4 17.5 1.0 CE1 A:HIS114 4.4 9.6 1.0 NE2 A:HIS114 4.5 9.1 1.0 O A:HOH451 4.6 13.6 1.0 CA A:CYS198 4.6 7.6 1.0 NE2 A:HIS179 4.7 7.5 1.0 C4 A:X8Z304 4.8 13.7 0.8 CE1 A:HIS179 4.9 9.9 1.0 OXT A:ACT307 5.0 12.8 1.0 C3 A:X8Z304 5.0 13.0 0.8

Zinc binding site 3 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with L- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:9.7 occ:1.00 O A:ACT305 1.9 13.2 1.0 O A:ACT306 2.0 10.7 1.0 ND1 A:HIS251 2.2 8.9 1.0 C A:ACT306 2.5 9.9 1.0 OXT A:ACT306 2.6 11.3 1.0 C A:ACT305 2.9 11.8 1.0 CE1 A:HIS251 3.1 11.8 1.0 CG A:HIS251 3.2 10.8 1.0 OXT A:ACT305 3.3 9.6 1.0 CB A:HIS251 3.5 9.1 1.0 CA A:HIS251 3.8 8.1 1.0 CH3 A:ACT306 4.1 13.7 1.0 NE2 A:HIS251 4.3 10.2 1.0 ND2 A:ASN254 4.3 10.8 1.0 CH3 A:ACT305 4.3 10.0 1.0 CD2 A:HIS251 4.3 9.9 1.0 CD2 A:LEU203 4.5 12.2 1.0 O A:HIS251 4.5 10.4 1.0 C A:HIS251 4.6 10.4 1.0 N A:HIS251 4.9 7.4 1.0

S.B.Silwal, B.Wamsley, Z.Wang, B.W.Gung, J.C.Nix, R.C.Page. Mutation of An Active Site-Adjacent Residue in Vim Indirectly Dictates Interactions with and Blunts Inhibition By D-Captopril. J.Inorg.Biochem. V. 271 12975 2025.
ISSN: ISSN 0162-0134
PubMed: 40513263
DOI: 10.1016/J.JINORGBIO.2025.112975