Zinc in PDB 7pp0: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 28 (Jmv-7038)

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 28 (Jmv-7038), PDB code: 7pp0 was solved by G.Tassone, M.Benvenuti, F.Verdirosa, G.Corsica, G.Chelini, F.De Luca, 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)	55.76 / 1.73
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.071, 78.128, 79.599, 90, 90, 90
R / Rfree (%)	17.6 / 21.8

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 28 (Jmv-7038) (pdb code 7pp0). 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 28 (Jmv-7038), PDB code: 7pp0:
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 28 (Jmv-7038)


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 28 (Jmv-7038) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.2 occ:1.00 NAE A:7ZN306 1.9 26.3 0.5 NAE A:7ZN306 1.9 25.0 0.5 ND1 A:HIS116 2.0 19.5 1.0 NE2 A:HIS179 2.0 16.5 1.0 NE2 A:HIS114 2.1 17.2 1.0 CAD A:7ZN306 2.9 26.0 0.5 CE1 A:HIS116 2.9 21.9 1.0 CAD A:7ZN306 2.9 25.4 0.5 CG A:HIS116 2.9 18.7 1.0 CD2 A:HIS179 3.0 14.3 1.0 NAB A:7ZN306 3.0 25.5 0.5 CD2 A:HIS114 3.0 15.8 1.0 NAB A:7ZN306 3.0 25.7 0.5 CE1 A:HIS179 3.0 18.8 1.0 CE1 A:HIS114 3.1 15.9 1.0 CB A:HIS116 3.3 17.5 1.0 SAF A:7ZN306 3.5 23.8 0.5 SAF A:7ZN306 3.5 23.5 0.5 NE2 A:HIS116 4.1 21.8 1.0 CAA A:7ZN306 4.1 27.4 0.5 CD2 A:HIS116 4.1 18.6 1.0 NAC A:7ZN306 4.1 26.7 0.5 CAA A:7ZN306 4.1 28.0 0.5 OD1 A:ASP118 4.1 23.4 1.0 NAC A:7ZN306 4.1 26.4 0.5 CG A:HIS179 4.1 15.6 1.0 ND1 A:HIS179 4.1 16.2 1.0 ND1 A:HIS114 4.1 15.4 1.0 CG A:HIS114 4.1 15.9 1.0 ZN A:ZN302 4.6 24.3 1.0 CB A:CYS198 4.7 21.6 1.0 O A:HOH492 4.7 46.8 1.0 CA A:HIS116 4.7 19.1 1.0 O A:HOH501 4.9 26.4 1.0 CG A:ASP118 4.9 21.2 1.0 N A:HIS116 5.0 18.8 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 28 (Jmv-7038)


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 28 (Jmv-7038) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.3 occ:1.00 OD2 A:ASP118 2.0 24.6 1.0 NE2 A:HIS240 2.2 20.4 1.0 SAF A:7ZN306 2.2 23.5 0.5 SG A:CYS198 2.2 22.0 1.0 SAF A:7ZN306 2.2 23.8 0.5 CAD A:7ZN306 3.0 25.4 0.5 CD2 A:HIS240 3.1 24.0 1.0 CG A:ASP118 3.1 21.2 1.0 CAD A:7ZN306 3.2 26.0 0.5 CE1 A:HIS240 3.2 24.1 1.0 CB A:CYS198 3.3 21.6 1.0 OD1 A:ASP118 3.6 23.4 1.0 NH2 A:ARG119 3.6 35.5 1.0 NAC A:7ZN306 3.7 26.4 0.5 CAG A:7ZN306 3.7 25.3 0.5 CAG A:7ZN306 3.7 25.9 0.5 NAC A:7ZN306 3.8 26.7 0.5 NE A:ARG119 3.8 26.0 1.0 NAE A:7ZN306 3.9 25.0 0.5 NAE A:7ZN306 4.1 26.3 0.5 CZ A:ARG119 4.1 29.2 1.0 O A:HOH429 4.2 22.7 1.0 CE1 A:HIS114 4.3 15.9 1.0 CG A:HIS240 4.3 21.0 1.0 ND1 A:HIS240 4.3 21.5 1.0 CB A:ASP118 4.3 21.9 1.0 CA A:CYS198 4.4 18.5 1.0 CAH A:7ZN306 4.6 26.1 0.5 ZN A:ZN301 4.6 19.2 1.0 CAI A:7ZN306 4.6 27.4 0.5 CAA A:7ZN306 4.7 28.0 0.5 CAH A:7ZN306 4.7 25.2 0.5 CAI A:7ZN306 4.8 25.6 0.5 NE2 A:HIS114 4.8 17.2 1.0 NAB A:7ZN306 4.8 25.7 0.5 CAN A:7ZN306 4.8 28.2 0.5 CAA A:7ZN306 4.9 27.4 0.5 CD A:ARG119 4.9 20.9 1.0 CAN A:7ZN306 4.9 26.1 0.5

Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 28 (Jmv-7038)


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 28 (Jmv-7038) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:20.8 occ:1.00 OXT A:ACT304 1.8 23.8 1.0 OXT A:ACT305 1.9 19.6 1.0 NE2 A:HIS153 2.0 18.9 1.0 C A:ACT305 2.6 19.5 1.0 O A:ACT305 2.8 21.4 1.0 C A:ACT304 2.9 26.9 1.0 CE1 A:HIS153 2.9 23.7 1.0 CD2 A:HIS153 3.1 21.6 1.0 O A:ACT304 3.2 23.0 1.0 ND1 A:HIS153 4.1 20.7 1.0 CB A:ALA132 4.1 18.7 1.0 CH3 A:ACT305 4.1 21.4 1.0 CG A:HIS153 4.2 19.7 1.0 CH3 A:ACT304 4.3 21.0 1.0 CA A:ALA132 4.7 20.7 1.0 O A:HOH443 4.9 29.8 1.0 CG2 A:THR152 5.0 20.9 1.0

F.Verdirosa, L.Gavara, L.Sevaille, G.Tassone, G.Corsica, A.Legru, G.Feller, G.Chelini, P.S.Mercuri, S.Tanfoni, F.Sannio, M.Benvenuti, G.Cerboni, F.De Luca, E.Bouajila, Y.Vo Hoang, P.Licznar-Fajardo, M.Galleni, C.Pozzi, S.Mangani, J.D.Docquier, J.F.Hernandez. 1,2,4-Triazole-3-Thione Analogues with A 2-Ethylbenzoic Acid at Position 4 As Vim-Type Metallo-Beta-Lactamase Inhibitors. Chemmedchem V. 17 00699 2022.
ISSN: ESSN 1860-7187
PubMed: 35050549
DOI: 10.1002/CMDC.202100699