Zinc in PDB 7ovf: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207)

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207), PDB code: 7ovf was solved by G.Tassone, M.Benvenuti, F.Verdirosa, F.Sannio, F.Marcoccia, J.D.Docquier, C.Pozzi, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.57 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.967, 78.069, 79.114, 90, 90, 90
R / Rfree (%)	18.4 / 26.3

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207) also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207) (pdb code 7ovf). 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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207), PDB code: 7ovf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.8 occ:1.00 NE2 A:HIS179 2.0 22.8 1.0 ND1 A:HIS116 2.0 24.1 1.0 NAB A:1TH306 2.0 38.0 1.0 NE2 A:HIS114 2.0 18.5 1.0 CE1 A:HIS114 2.9 17.3 1.0 CE1 A:HIS116 3.0 24.4 1.0 CG A:HIS116 3.0 23.6 1.0 CD2 A:HIS179 3.0 19.8 1.0 CAE A:1TH306 3.0 37.8 1.0 CE1 A:HIS179 3.0 22.9 1.0 NAA A:1TH306 3.0 33.0 1.0 CD2 A:HIS114 3.1 19.0 1.0 CB A:HIS116 3.3 21.6 1.0 SAF A:1TH306 3.6 33.5 1.0 OD1 A:ASP118 4.0 28.6 1.0 ND1 A:HIS114 4.1 19.5 1.0 NE2 A:HIS116 4.1 23.4 1.0 CD2 A:HIS116 4.1 25.1 1.0 CG A:HIS179 4.1 20.0 1.0 ND1 A:HIS179 4.1 20.7 1.0 CAC A:1TH306 4.1 40.3 1.0 CG A:HIS114 4.1 19.4 1.0 NAD A:1TH306 4.1 38.4 1.0 ND2 A:ASN210 4.4 59.9 1.0 ZN A:ZN302 4.6 32.2 1.0 CB A:CYS198 4.7 28.2 1.0 CA A:HIS116 4.7 25.3 1.0 O A:HOH466 4.9 25.8 1.0 CG A:ASP118 4.9 27.2 1.0 OD2 A:ASP118 5.0 30.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:32.2 occ:1.00 OD2 A:ASP118 2.0 30.8 1.0 NE2 A:HIS240 2.2 24.5 1.0 SG A:CYS198 2.2 28.2 1.0 SAF A:1TH306 2.3 33.5 1.0 CD2 A:HIS240 3.1 27.1 1.0 CG A:ASP118 3.2 27.2 1.0 CE1 A:HIS240 3.2 27.4 1.0 CAE A:1TH306 3.2 37.8 1.0 CB A:CYS198 3.3 28.2 1.0 OD1 A:ASP118 3.7 28.6 1.0 NH2 A:ARG119 3.7 36.4 1.0 NAD A:1TH306 3.8 38.4 1.0 CAM A:1TH306 3.8 43.7 1.0 NE A:ARG119 3.9 28.6 1.0 NAB A:1TH306 4.1 38.0 1.0 CZ A:ARG119 4.1 28.6 1.0 CG A:HIS240 4.3 24.0 1.0 ND1 A:HIS240 4.3 26.6 1.0 O A:HOH474 4.4 34.9 1.0 CB A:ASP118 4.4 26.5 1.0 CE1 A:HIS114 4.4 17.3 1.0 CA A:CYS198 4.5 25.2 1.0 ZN A:ZN301 4.6 22.8 1.0 CAC A:1TH306 4.8 40.3 1.0 CD A:ARG119 4.9 24.7 1.0 NAA A:1TH306 5.0 33.0 1.0 CAP A:1TH306 5.0 58.8 1.0 NE2 A:HIS114 5.0 18.5 1.0 NE2 A:HIS179 5.0 22.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207)


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 Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7207) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:25.0 occ:1.00 OXT A:ACT304 1.8 27.1 1.0 OXT A:ACT305 2.1 24.9 1.0 NE2 A:HIS153 2.1 22.4 1.0 O A:ACT305 2.7 25.5 1.0 C A:ACT305 2.7 28.5 1.0 C A:ACT304 2.9 28.1 1.0 CE1 A:HIS153 2.9 26.8 1.0 CD2 A:HIS153 3.2 22.8 1.0 O A:ACT304 3.3 24.8 1.0 CB A:ALA132 4.1 22.6 1.0 ND1 A:HIS153 4.1 25.5 1.0 CH3 A:ACT305 4.2 25.2 1.0 CH3 A:ACT304 4.2 25.4 1.0 CG A:HIS153 4.2 23.4 1.0 CA A:ALA132 4.7 23.7 1.0 O A:HOH404 4.9 35.7 1.0 CG2 A:THR152 4.9 25.8 1.0

A.Legru, F.Verdirosa, J.F.Hernandez, G.Tassone, F.Sannio, M.Benvenuti, P.A.Conde, G.Bossis, C.A.Thomas, M.W.Crowder, M.Dillenberger, K.Becker, C.Pozzi, S.Mangani, J.D.Docquier, L.Gavara. 1,2,4-Triazole-3-Thione Compounds with A 4-Ethyl Alkyl/Aryl Sulfide Substituent Are Broad-Spectrum Metallo-Beta-Lactamase Inhibitors with Re-Sensitization Activity. Eur.J.Med.Chem. V. 226 13873 2021.
ISSN: ISSN 0223-5234
PubMed: 34626878
DOI: 10.1016/J.EJMECH.2021.113873