Zinc in PDB 9cv2: Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with D- Captopril

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with D- Captopril, PDB code: 9cv2 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)	39.43 / 1.57
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.642, 77.318, 78.854, 90, 90, 90
R / Rfree (%)	16.7 / 18.1

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with D- Captopril (pdb code 9cv2). 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 D- Captopril, PDB code: 9cv2:
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 D- 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 D- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.0 occ:1.00 NE2 A:HIS179 2.1 13.1 1.0 ND1 A:HIS116 2.1 17.1 1.0 NE2 A:HIS114 2.1 15.0 1.0 S A:MCO304 2.3 19.3 0.5 S A:MCO304 2.3 19.2 0.5 CE1 A:HIS179 3.0 14.9 1.0 C1 A:MCO304 3.0 22.6 0.5 CD2 A:HIS179 3.1 12.3 1.0 CD2 A:HIS114 3.1 12.5 1.0 CE1 A:HIS114 3.1 12.9 1.0 CG A:HIS116 3.1 16.3 1.0 CE1 A:HIS116 3.1 17.1 1.0 C1 A:MCO304 3.2 22.4 0.5 CB A:HIS116 3.4 15.9 1.0 ZN A:ZN302 3.7 17.3 1.0 CB A:CYS198 4.0 14.1 1.0 OD1 A:ASP118 4.0 17.1 1.0 ND1 A:HIS179 4.1 15.0 1.0 ND1 A:HIS114 4.2 13.7 1.0 CG A:HIS179 4.2 12.7 1.0 CG A:HIS114 4.2 12.9 1.0 NE2 A:HIS116 4.2 17.7 1.0 CD2 A:HIS116 4.2 16.3 1.0 SG A:CYS198 4.3 14.8 1.0 C2 A:MCO304 4.5 24.8 0.5 C2 A:MCO304 4.6 24.8 0.5 OD2 A:ASP118 4.7 18.6 1.0 CG A:ASP118 4.8 18.3 1.0 CA A:HIS116 4.8 13.8 1.0 ND2 A:ASN210 4.8 27.5 1.0 O1 A:MCO304 4.9 28.7 0.5 O1 A:MCO304 5.0 28.7 0.5 O A:HOH471 5.0 32.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with D- 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 D- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.3 occ:1.00 OD2 A:ASP118 2.0 18.6 1.0 NE2 A:HIS240 2.2 16.8 1.0 SG A:CYS198 2.2 14.8 1.0 S A:MCO304 2.3 19.2 0.5 S A:MCO304 2.3 19.3 0.5 CG A:ASP118 3.0 18.3 1.0 CE1 A:HIS240 3.1 17.7 1.0 CD2 A:HIS240 3.2 16.1 1.0 C1 A:MCO304 3.3 22.4 0.5 CB A:CYS198 3.3 14.1 1.0 OD1 A:ASP118 3.4 17.1 1.0 C1 A:MCO304 3.4 22.6 0.5 ZN A:ZN301 3.7 15.0 1.0 NH2 A:ARG119 3.7 18.5 1.0 C2 A:MCO304 3.9 24.8 0.5 C2 A:MCO304 3.9 24.8 0.5 NE A:ARG119 4.0 16.5 1.0 ND1 A:HIS240 4.2 17.9 1.0 CG A:HIS240 4.3 14.1 1.0 CE1 A:HIS114 4.3 12.9 1.0 CZ A:ARG119 4.3 17.4 1.0 CB A:ASP118 4.3 17.6 1.0 NE2 A:HIS114 4.4 15.0 1.0 C4 A:MCO304 4.6 29.1 0.5 CA A:CYS198 4.6 12.1 1.0 NE2 A:HIS179 4.6 13.1 1.0 C5 A:MCO304 4.6 28.2 0.5 C4 A:MCO304 4.7 29.2 0.5 O A:HOH469 4.7 18.2 1.0 CE1 A:HIS179 4.8 14.9 1.0 O A:HOH402 4.9 14.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-20 with D- 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 D- Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:17.7 occ:1.00 O A:HOH529 2.1 11.6 1.0 ND1 A:HIS251 2.1 14.0 1.0 O A:HOH528 2.2 11.3 1.0 CE1 A:HIS251 3.0 21.6 1.0 CG A:HIS251 3.2 17.3 1.0 CB A:HIS251 3.6 17.1 1.0 CA A:HIS251 3.9 17.2 1.0 NE2 A:HIS251 4.1 16.5 1.0 CD2 A:HIS251 4.3 18.9 1.0 O A:HIS251 4.4 17.2 1.0 C A:HIS251 4.6 17.2 1.0 ND2 A:ASN254 4.8 24.0 1.0 O A:LEU203 4.9 20.1 1.0 CD2 A:LEU203 4.9 22.0 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