Zinc in PDB 7ove: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210)

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210), PDB code: 7ove was solved by G.Tassone, M.Benvenuti, F.Verdirosa, F.Sannio, S.Mangani, J.D.Docquier, C.Pozzi, F.Marcoccia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.40 / 1.92
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.116, 78.133, 79.3, 90, 90, 90
R / Rfree (%)	19 / 24.7

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 10 (Jmv-7210) (pdb code 7ove). 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 10 (Jmv-7210), PDB code: 7ove:
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 10 (Jmv-7210)


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 10 (Jmv-7210) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.4 occ:1.00 ND1 A:HIS116 2.0 17.5 1.0 NE2 A:HIS179 2.0 15.7 1.0 NAI A:UNL306 2.0 54.0 1.0 NE2 A:HIS114 2.1 14.2 1.0 CE1 A:HIS114 2.9 13.7 1.0 NAH A:UNL306 2.9 51.7 1.0 CE1 A:HIS116 3.0 21.2 1.0 CG A:HIS116 3.0 18.3 1.0 CE1 A:HIS179 3.0 15.2 1.0 CD2 A:HIS179 3.0 14.3 1.0 CAJ A:UNL306 3.1 54.1 1.0 CD2 A:HIS114 3.2 15.7 1.0 CB A:HIS116 3.3 18.3 1.0 SAW A:UNL306 3.7 47.5 1.0 OD1 A:ASP118 4.0 27.9 1.0 ND1 A:HIS114 4.1 15.4 1.0 CAG A:UNL306 4.1 56.3 1.0 NE2 A:HIS116 4.1 18.8 1.0 CD2 A:HIS116 4.1 19.8 1.0 ND1 A:HIS179 4.1 14.8 1.0 NAK A:UNL306 4.2 57.0 1.0 CG A:HIS179 4.2 14.4 1.0 CG A:HIS114 4.2 15.1 1.0 ZN A:ZN302 4.5 35.3 1.0 CB A:CYS198 4.7 22.6 1.0 CA A:HIS116 4.7 20.1 1.0 ND2 A:ASN210 4.8 52.5 0.7 SG A:CYS198 4.8 26.6 1.0 CG A:ASP118 4.9 27.2 1.0 O A:HOH500 4.9 27.0 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 10 (Jmv-7210)


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 10 (Jmv-7210) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:35.3 occ:1.00 SG A:CYS198 2.2 26.6 1.0 NE2 A:HIS240 2.2 25.7 1.0 OD2 A:ASP118 2.2 27.4 1.0 SAW A:UNL306 2.3 47.5 1.0 CD2 A:HIS240 3.1 28.2 1.0 CAJ A:UNL306 3.1 54.1 1.0 CE1 A:HIS240 3.2 27.5 1.0 CG A:ASP118 3.3 27.2 1.0 CB A:CYS198 3.3 22.6 1.0 NH2 A:ARG119 3.5 33.5 1.0 NAK A:UNL306 3.7 57.0 1.0 OD1 A:ASP118 3.7 27.9 1.0 CAL A:UNL306 3.8 54.7 1.0 NE A:ARG119 3.8 24.8 1.0 NAI A:UNL306 4.0 54.0 1.0 CZ A:ARG119 4.1 29.6 1.0 CG A:HIS240 4.3 24.6 1.0 ND1 A:HIS240 4.3 26.1 1.0 O A:HOH453 4.4 31.4 1.0 CA A:CYS198 4.5 20.4 1.0 CE1 A:HIS114 4.5 13.7 1.0 ZN A:ZN301 4.5 19.4 1.0 CB A:ASP118 4.6 25.1 1.0 CAM A:UNL306 4.7 53.0 1.0 CAG A:UNL306 4.7 56.3 1.0 NAH A:UNL306 4.9 51.7 1.0 NE2 A:HIS179 4.9 15.7 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 10 (Jmv-7210)


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 10 (Jmv-7210) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:21.4 occ:1.00 O A:ACT304 1.8 23.5 1.0 NE2 A:HIS153 2.0 19.5 1.0 OXT A:ACT305 2.1 21.2 1.0 O A:ACT305 2.6 21.6 1.0 C A:ACT305 2.7 23.3 1.0 C A:ACT304 2.9 23.6 1.0 CE1 A:HIS153 3.0 23.0 1.0 CD2 A:HIS153 3.0 18.8 1.0 OXT A:ACT304 3.2 21.7 1.0 ND1 A:HIS153 4.1 19.7 1.0 CG A:HIS153 4.2 19.4 1.0 CH3 A:ACT305 4.2 22.8 1.0 CB A:ALA132 4.2 21.0 1.0 CH3 A:ACT304 4.2 21.6 1.0 CA A:ALA132 4.7 21.9 1.0 O A:HOH420 4.8 31.7 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