Zinc in PDB 8a76: Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26

The structure of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26, PDB code: 8a76 was solved by F.Vascon, A.Legru, J.F.Hernandez, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.57 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.332, 73.904, 77.288, 90, 90, 90
R / Rfree (%)	16.6 / 18.8

The structure of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 (pdb code 8a76). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26, PDB code: 8a76:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.7 occ:0.80 ND1 A:HIS122 1.7 23.0 1.0 NE2 A:HIS120 2.0 22.2 1.0 N3 A:L82304 2.1 34.7 0.8 NE2 A:HIS189 2.1 24.9 1.0 C13 A:L82304 2.8 33.7 0.8 CE1 A:HIS122 2.8 21.9 1.0 CG A:HIS122 2.9 22.9 1.0 CE1 A:HIS120 2.9 18.9 1.0 CD2 A:HIS189 3.0 23.4 1.0 CD2 A:HIS120 3.0 20.1 1.0 CE1 A:HIS189 3.1 27.6 1.0 N2 A:L82304 3.2 33.3 0.8 S1 A:L82304 3.2 33.1 0.8 CB A:HIS122 3.3 20.7 1.0 ZN A:ZN302 4.0 20.6 0.8 NE2 A:HIS122 4.0 24.8 1.0 CD2 A:HIS122 4.0 24.6 1.0 OD1 A:ASP124 4.0 22.2 1.0 N1 A:L82304 4.0 33.0 0.8 ND1 A:HIS120 4.1 20.9 1.0 CG A:HIS120 4.1 18.8 1.0 CG A:HIS189 4.2 20.7 1.0 C6 A:L82304 4.2 32.8 0.8 ND1 A:HIS189 4.2 22.1 1.0 SG A:CYS208 4.3 21.2 1.0 CG2 A:THR190 4.4 19.7 1.0 CB A:CYS208 4.4 19.8 1.0 OD2 A:ASP124 4.8 23.4 1.0 CA A:HIS122 4.8 18.9 1.0 CG A:ASP124 4.8 22.0 1.0

Zinc binding site 2 out of 4 in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.6 occ:0.80 OD2 A:ASP124 2.0 23.4 1.0 NE2 A:HIS250 2.0 21.6 1.0 S1 A:L82304 2.1 33.1 0.8 SG A:CYS208 2.2 21.2 1.0 C13 A:L82304 2.9 33.7 0.8 CE1 A:HIS250 3.0 22.7 1.0 CD2 A:HIS250 3.0 24.0 1.0 CG A:ASP124 3.0 22.0 1.0 CB A:CYS208 3.4 19.8 1.0 OD1 A:ASP124 3.4 22.2 1.0 N1 A:L82304 3.5 33.0 0.8 C5 A:L82304 3.7 31.4 0.8 N3 A:L82304 3.7 34.7 0.8 ZN A:ZN301 4.0 23.7 0.8 CB A:SER249 4.1 18.0 1.0 ND1 A:HIS250 4.1 22.7 1.0 CG A:HIS250 4.2 21.3 1.0 CB A:ASP124 4.3 19.2 1.0 CE1 A:HIS120 4.4 18.9 1.0 OG A:SER249 4.5 19.8 1.0 CA A:CYS208 4.5 17.7 1.0 C6 A:L82304 4.5 32.8 0.8 O A:HOH401 4.6 45.4 1.0 NE2 A:HIS189 4.6 24.9 1.0 NE2 A:HIS120 4.7 22.2 1.0 N2 A:L82304 4.7 33.3 0.8 C4 A:L82304 4.7 34.2 0.8 CE A:LYS125 4.8 18.4 1.0 CE1 A:HIS189 4.9 27.6 1.0 CD A:LYS125 5.0 18.1 1.0

Zinc binding site 3 out of 4 in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:18.9 occ:0.85 O B:HOH442 1.9 21.2 1.0 ND1 B:HIS122 2.0 22.9 1.0 NE2 B:HIS120 2.0 20.2 1.0 NE2 B:HIS189 2.1 19.9 1.0 CD2 B:HIS189 3.0 18.0 1.0 CE1 B:HIS120 3.0 18.8 1.0 CE1 B:HIS122 3.0 21.4 1.0 CG B:HIS122 3.1 21.6 1.0 CD2 B:HIS120 3.1 18.6 1.0 CE1 B:HIS189 3.1 20.6 1.0 CB B:HIS122 3.4 17.6 1.0 ZN B:ZN302 3.6 22.4 0.8 O B:HOH526 3.9 38.4 1.0 OD1 B:ASP124 3.9 21.3 1.0 SG B:CYS208 3.9 20.8 1.0 ND1 B:HIS120 4.1 20.1 1.0 CB B:CYS208 4.2 17.6 1.0 CG B:HIS189 4.2 19.6 1.0 CG B:HIS120 4.2 18.6 1.0 ND1 B:HIS189 4.2 18.9 1.0 NE2 B:HIS122 4.2 22.5 1.0 CD2 B:HIS122 4.2 22.6 1.0 CG2 B:THR190 4.5 18.3 1.0 OD2 B:ASP124 4.5 22.9 1.0 CG B:ASP124 4.7 22.1 1.0 CA B:HIS122 4.8 18.2 1.0

Zinc binding site 4 out of 4 in the Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metallo-Beta-Lactamase Ndm-1 in Complex with 1,2,4-Triazole-3-Thione Compound 26 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.4 occ:0.85 NE2 B:HIS250 2.0 21.1 1.0 OD2 B:ASP124 2.0 22.9 1.0 O B:HOH442 2.1 21.2 1.0 SG B:CYS208 2.3 20.8 1.0 O B:HOH526 2.4 38.4 1.0 CD2 B:HIS250 3.0 20.4 1.0 CG B:ASP124 3.0 22.1 1.0 CE1 B:HIS250 3.0 21.3 1.0 OD1 B:ASP124 3.4 21.3 1.0 CB B:CYS208 3.4 17.6 1.0 ZN B:ZN301 3.6 18.9 0.8 CG B:HIS250 4.1 21.2 1.0 ND1 B:HIS250 4.1 21.2 1.0 CB B:SER249 4.2 17.1 1.0 CB B:ASP124 4.3 17.5 1.0 NE2 B:HIS189 4.3 19.9 1.0 OG B:SER249 4.5 18.4 1.0 CE1 B:HIS189 4.5 20.6 1.0 NE2 B:HIS120 4.6 20.2 1.0 CA B:CYS208 4.6 18.5 1.0 CE1 B:HIS120 4.6 18.8 1.0 CE B:LYS125 4.9 19.9 1.0 CD B:LYS125 5.0 19.8 1.0

A.Legru, F.Verdirosa, Y.Vo-Hoang, G.Tassone, F.Vascon, C.A.Thomas, F.Sannio, G.Corsica, M.Benvenuti, G.Feller, R.Coulon, F.Marcoccia, S.R.Devente, E.Bouajila, C.Piveteau, F.Leroux, R.Deprez-Poulain, B.Deprez, P.Licznar-Fajardo, M.W.Crowder, L.Cendron, C.Pozzi, S.Mangani, J.D.Docquier, J.F.Hernandez, L.Gavara. Optimization of 1,2,4-Triazole-3-Thiones Toward Broad-Spectrum Metallo-Beta-Lactamase Inhibitors Showing Potent Synergistic Activity on Vim- and Ndm-1-Producing Clinical Isolates. J.Med.Chem. V. 65 16392 2022.
ISSN: ISSN 0022-2623
PubMed: 36450011
DOI: 10.1021/ACS.JMEDCHEM.2C01257