Calcium 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:

Zinc

(Zn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca303 b:30.0 occ:1.00 O B:HOH447 2.2 43.1 1.0 O A:HOH520 2.3 38.6 1.0 OD2 A:ASP223 2.4 35.4 1.0 O A:HOH402 2.4 37.7 1.0 OE2 B:GLU227 2.5 36.4 1.0 OE1 B:GLU227 2.6 45.9 1.0 OE1 A:GLU152 2.7 27.7 1.0 OE2 A:GLU152 2.7 26.5 1.0 CD B:GLU227 2.9 37.5 1.0 OD1 A:ASP223 3.0 45.2 1.0 CG A:ASP223 3.0 39.8 1.0 CD A:GLU152 3.0 26.8 1.0 O2 A:EDO307 4.4 31.3 1.0 NE2 A:HIS122 4.4 24.8 1.0 CG B:GLU227 4.4 26.4 1.0 CB A:ASP223 4.5 30.8 1.0 CG A:GLU152 4.6 22.2 1.0 NE2 B:HIS228 4.6 20.3 1.0 O A:HOH424 4.7 27.7 1.0 CE1 B:HIS228 4.7 21.6 1.0 CD2 A:HIS122 5.0 24.6 1.0 O B:HOH530 5.0 35.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca313 b:32.6 occ:1.00 O A:HOH526 2.2 40.6 1.0 OD2 A:ASP130 2.3 31.6 1.0 OD2 A:ASP95 2.3 24.7 1.0 O A:HOH512 2.5 23.8 1.0 O A:HOH425 2.6 32.5 1.0 O A:HOH417 2.7 41.1 1.0 CG A:ASP130 3.3 24.9 1.0 CG A:ASP95 3.4 23.7 1.0 CB A:ASP130 3.8 22.6 1.0 OD1 A:ASP95 3.8 22.3 1.0 O A:GLY127 4.3 20.6 1.0 O A:HOH483 4.3 28.0 1.0 OD1 A:ASP130 4.4 26.8 1.0 O A:HOH438 4.5 28.3 1.0 O A:HOH456 4.5 21.7 1.0 CG2 A:VAL155 4.7 24.2 1.0 N A:ASP130 4.7 18.9 1.0 CB A:ASP95 4.7 20.4 1.0 CA A:ASP130 4.9 21.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca303 b:52.1 occ:1.00 OD2 B:ASP95 2.4 26.3 1.0 O B:HOH517 2.7 25.7 1.0 OD2 B:ASP130 2.8 28.6 1.0 CG B:ASP95 3.4 24.5 1.0 CG B:ASP130 3.4 22.0 1.0 CB B:ASP130 3.7 17.4 1.0 OD1 B:ASP95 3.8 23.9 1.0 O B:HOH412 3.9 22.4 1.0 OD1 B:ASP130 4.3 22.7 1.0 O B:HOH491 4.4 27.6 1.0 O B:GLY127 4.4 19.8 1.0 O B:HOH456 4.6 28.1 1.0 N B:ASP130 4.7 16.5 1.0 CB B:ASP95 4.7 19.3 1.0 CG2 B:VAL155 4.7 17.8 1.0 O B:HOH471 4.8 21.0 1.0 CA B:ASP130 4.9 15.7 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:25.7 occ:1.00 O A:HOH422 2.2 34.7 1.0 O B:HOH518 2.3 38.3 1.0 O B:HOH433 2.3 36.8 1.0 OD2 B:ASP223 2.4 16.8 0.5 OE2 B:GLU152 2.5 22.5 1.0 OE2 A:GLU227 2.5 34.0 1.0 OE1 B:GLU152 2.5 23.3 1.0 OD1 B:ASP223 2.8 20.6 0.5 OE1 A:GLU227 2.8 48.1 1.0 OD1 B:ASP223 2.8 28.1 0.5 CD B:GLU152 2.9 21.5 1.0 CG B:ASP223 2.9 18.1 0.5 CD A:GLU227 3.0 35.5 1.0 CG B:ASP223 3.3 31.2 0.5 OD2 B:ASP223 3.5 36.4 0.5 O2 B:EDO307 4.4 34.9 1.0 NE2 B:HIS122 4.4 22.5 1.0 CG B:GLU152 4.4 19.6 1.0 CB B:ASP223 4.5 20.3 0.5 CG A:GLU227 4.5 29.7 1.0 CB B:ASP223 4.5 29.1 0.5 O B:HOH438 4.5 27.5 1.0 NE2 A:HIS228 4.5 19.1 1.0 C2 B:EDO307 4.6 44.8 1.0 CE1 A:HIS228 4.8 19.3 1.0 CD2 B:HIS122 4.9 22.6 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