Zinc in PDB 6yrp: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Jmv-4690 (Cpd 31)

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Jmv-4690 (Cpd 31), PDB code: 6yrp was solved by J.D.Docquier, C.Pozzi, F.De Luca, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.07 / 1.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.140, 79.000, 79.690, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 23.6

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Jmv-4690 (Cpd 31) (pdb code 6yrp). 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 Jmv-4690 (Cpd 31), PDB code: 6yrp:
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 Jmv-4690 (Cpd 31)


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 Jmv-4690 (Cpd 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.8 occ:1.00 ND1 A:HIS118 1.9 13.2 1.0 N5 A:PJB404 1.9 26.8 1.0 NE2 A:HIS116 2.0 10.1 1.0 NE2 A:HIS196 2.1 9.6 1.0 C3 A:PJB404 2.9 25.0 1.0 CE1 A:HIS118 2.9 16.1 1.0 CG A:HIS118 2.9 13.1 1.0 CE1 A:HIS116 3.0 10.1 1.0 CD2 A:HIS116 3.0 10.9 1.0 CD2 A:HIS196 3.0 9.7 1.0 N4 A:PJB404 3.0 22.8 1.0 CE1 A:HIS196 3.2 10.2 1.0 CB A:HIS118 3.3 12.0 1.0 S6 A:PJB404 3.3 22.3 1.0 N2 A:PJB404 4.0 26.5 1.0 NE2 A:HIS118 4.0 14.7 1.0 CD2 A:HIS118 4.0 14.7 1.0 ND1 A:HIS116 4.1 10.5 1.0 CG A:HIS116 4.1 10.6 1.0 C1 A:PJB404 4.1 24.9 1.0 OD1 A:ASP120 4.2 17.1 1.0 CG A:HIS196 4.2 9.2 1.0 ND1 A:HIS196 4.2 9.6 1.0 ZN A:ZN402 4.7 19.1 1.0 CA A:HIS118 4.7 12.6 1.0 CB A:CYS221 4.8 13.2 1.0 O A:HOH563 4.9 13.9 1.0 O A:HOH572 5.0 31.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Jmv-4690 (Cpd 31)


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 Jmv-4690 (Cpd 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.1 occ:1.00 OD2 A:ASP120 2.1 17.4 1.0 SG A:CYS221 2.2 14.1 1.0 S6 A:PJB404 2.2 22.3 1.0 NE2 A:HIS263 2.3 16.8 1.0 C3 A:PJB404 3.2 25.0 1.0 CB A:CYS221 3.2 13.2 1.0 CG A:ASP120 3.2 16.6 1.0 CD2 A:HIS263 3.3 17.3 1.0 CE1 A:HIS263 3.3 16.4 1.0 OD1 A:ASP120 3.7 17.1 1.0 N7 A:PJB404 3.7 27.8 1.0 N2 A:PJB404 3.8 26.5 1.0 NE A:ARG121 3.8 18.1 1.0 NH2 A:ARG121 4.0 22.2 1.0 N5 A:PJB404 4.0 26.8 1.0 C8 A:PJB404 4.1 30.4 1.0 CE1 A:HIS116 4.1 10.1 1.0 CZ A:ARG121 4.2 20.0 1.0 O A:HOH519 4.3 16.1 1.0 CA A:CYS221 4.4 12.3 1.0 ND1 A:HIS263 4.4 14.2 1.0 CG A:HIS263 4.4 15.2 1.0 CB A:ASP120 4.4 16.1 1.0 C9 A:PJB404 4.6 34.2 1.0 ZN A:ZN401 4.7 12.8 1.0 CD A:ARG121 4.7 17.6 1.0 NE2 A:HIS116 4.8 10.1 1.0 C1 A:PJB404 4.9 24.9 1.0 N A:CYS221 5.0 11.9 1.0 C10 A:PJB404 5.0 36.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Jmv-4690 (Cpd 31)


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 Jmv-4690 (Cpd 31) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:16.4 occ:1.00 O A:ACT408 1.8 17.9 1.0 O A:ACT409 2.0 19.6 1.0 ND1 A:HIS285 2.2 14.4 1.0 C A:ACT409 2.7 20.7 1.0 OXT A:ACT409 2.7 19.2 1.0 C A:ACT408 2.8 19.1 1.0 CE1 A:HIS285 3.1 14.3 1.0 OXT A:ACT408 3.2 16.6 1.0 CG A:HIS285 3.2 14.5 1.0 CB A:HIS285 3.6 15.5 1.0 CA A:HIS285 3.8 15.0 1.0 CH3 A:ACT408 4.2 18.4 1.0 CH3 A:ACT409 4.2 21.3 1.0 OD1 A:ASN288 4.3 17.3 1.0 NE2 A:HIS285 4.3 12.5 1.0 CD2 A:HIS285 4.3 14.5 1.0 CD2 A:LEU226 4.4 18.9 1.0 O A:HIS285 4.6 14.1 1.0 C A:HIS285 4.7 15.2 1.0 N A:HIS285 4.9 16.2 1.0

L.Gavara, L.Sevaille, F.De Luca, P.Mercuri, C.Bebrone, G.Feller, A.Legru, G.Cerboni, S.Tanfoni, D.Baud, G.Cutolo, B.Bestgen, G.Chelini, F.Verdirosa, F.Sannio, C.Pozzi, M.Benvenuti, K.Kwapien, M.Fischer, K.Becker, J.M.Frere, S.Mangani, N.Gresh, D.Berthomieu, M.Galleni, J.D.Docquier, J.F.Hernandez. 4-Amino-1,2,4-Triazole-3-Thione-Derived Schiff Bases As Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 208 12720 2020.
ISSN: ISSN 0223-5234
PubMed: 32937203
DOI: 10.1016/J.EJMECH.2020.112720