Zinc in PDB 6tgd: Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31

The structure of Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31, PDB code: 6tgd was solved by L.Maso, F.Spirakis, M.Santucci, C.Simon, J.D.Docquier, G.Cruciani, M.P.Costi, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.42 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.678, 73.665, 77.501, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.7

The structure of Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31 (pdb code 6tgd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31, PDB code: 6tgd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 Ndm-1 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.0 occ:1.00 ND1 A:HIS122 1.9 16.6 1.0 NE2 A:HIS120 2.0 16.9 1.0 NE2 A:HIS189 2.0 16.1 1.0 N04 A:N8Q305 2.2 30.7 1.0 CE1 A:HIS122 2.9 17.1 1.0 CE1 A:HIS120 2.9 17.4 1.0 CG A:HIS122 3.0 16.4 1.0 CD2 A:HIS189 3.0 17.1 1.0 CD2 A:HIS120 3.1 15.3 1.0 CE1 A:HIS189 3.1 18.0 1.0 N05 A:N8Q305 3.1 26.2 1.0 C13 A:N8Q305 3.2 25.7 1.0 CB A:HIS122 3.3 15.7 1.0 S01 A:N8Q305 3.8 22.5 1.0 ND1 A:HIS120 4.1 15.8 1.0 NE2 A:HIS122 4.1 18.7 1.0 CD2 A:HIS122 4.1 16.5 1.0 OD1 A:ASP124 4.1 17.5 1.0 CG A:HIS120 4.1 15.3 1.0 ND1 A:HIS189 4.2 15.8 1.0 CG A:HIS189 4.2 14.3 1.0 C12 A:N8Q305 4.2 27.7 1.0 N03 A:N8Q305 4.2 27.8 1.0 CG2 A:THR190 4.3 15.1 1.0 ZN A:ZN302 4.4 16.8 1.0 SG A:CYS208 4.6 15.0 1.0 CB A:CYS208 4.6 14.3 1.0 CA A:HIS122 4.8 14.6 1.0 O A:HOH490 4.8 27.0 1.0 CG A:ASP124 5.0 15.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 Ndm-1 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.8 occ:1.00 OD2 A:ASP124 2.0 15.1 1.0 NE2 A:HIS250 2.1 16.8 1.0 S01 A:N8Q305 2.2 22.5 1.0 SG A:CYS208 2.3 15.0 1.0 C13 A:N8Q305 2.8 25.7 1.0 CG A:ASP124 3.0 15.8 1.0 CE1 A:HIS250 3.0 16.2 1.0 CD2 A:HIS250 3.1 15.2 1.0 CB A:CYS208 3.3 14.3 1.0 OD1 A:ASP124 3.4 17.5 1.0 N03 A:N8Q305 3.5 27.8 1.0 C10 A:N8Q305 3.6 29.8 1.0 N04 A:N8Q305 3.7 30.7 1.0 CB A:SER249 4.1 13.8 1.0 ND1 A:HIS250 4.2 15.7 1.0 CG A:HIS250 4.2 16.0 1.0 CB A:ASP124 4.3 14.5 1.0 ZN A:ZN301 4.4 20.0 1.0 CA A:CYS208 4.5 14.7 1.0 OG A:SER249 4.5 14.7 1.0 C12 A:N8Q305 4.5 27.7 1.0 CE1 A:HIS120 4.6 17.4 1.0 N05 A:N8Q305 4.6 26.2 1.0 NE2 A:HIS189 4.7 16.1 1.0 O A:HOH492 4.8 33.2 1.0 C08 A:N8Q305 4.8 35.1 1.0 C07 A:N8Q305 4.8 36.0 1.0 NE2 A:HIS120 5.0 16.9 1.0 CE1 A:HIS189 5.0 18.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


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 Ndm-1 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:20.3 occ:1.00 ND1 B:HIS122 2.0 20.0 1.0 NE2 B:HIS189 2.0 16.8 1.0 NE2 B:HIS120 2.1 15.3 1.0 N04 B:N8Q305 2.1 34.1 1.0 CG B:HIS122 3.0 16.6 1.0 N05 B:N8Q305 3.0 32.3 1.0 CE1 B:HIS122 3.0 16.2 1.0 CD2 B:HIS189 3.0 16.6 1.0 CE1 B:HIS120 3.1 16.0 1.0 CD2 B:HIS120 3.1 13.9 1.0 CE1 B:HIS189 3.1 18.9 1.0 C13 B:N8Q305 3.1 35.6 1.0 CB B:HIS122 3.3 15.2 1.0 S01 B:N8Q305 3.7 26.1 1.0 C12 B:N8Q305 4.1 30.5 1.0 NE2 B:HIS122 4.1 17.2 1.0 CD2 B:HIS122 4.1 18.1 1.0 N03 B:N8Q305 4.1 29.4 1.0 ND1 B:HIS120 4.2 16.4 1.0 CG B:HIS189 4.2 15.1 1.0 ND1 B:HIS189 4.2 17.2 1.0 OD1 B:ASP124 4.2 16.1 1.0 CG B:HIS120 4.2 15.1 1.0 CG2 B:THR190 4.3 16.5 1.0 ZN B:ZN302 4.5 17.6 1.0 SG B:CYS208 4.7 16.0 1.0 CB B:CYS208 4.7 13.8 1.0 O B:HOH479 4.8 29.7 1.0 CA B:HIS122 4.8 13.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 in Complex with Triazole-Based Inhibitor OP31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.6 occ:1.00 OD2 B:ASP124 2.0 15.6 1.0 NE2 B:HIS250 2.0 15.7 1.0 S01 B:N8Q305 2.2 26.1 1.0 SG B:CYS208 2.3 16.0 1.0 C13 B:N8Q305 2.9 35.6 1.0 CE1 B:HIS250 3.0 15.1 1.0 CD2 B:HIS250 3.0 14.3 1.0 CG B:ASP124 3.0 15.5 1.0 CB B:CYS208 3.3 13.8 1.0 C10 B:N8Q305 3.4 32.3 1.0 N03 B:N8Q305 3.4 29.4 1.0 OD1 B:ASP124 3.5 16.1 1.0 N04 B:N8Q305 3.8 34.1 1.0 CB B:SER249 4.1 13.6 1.0 ND1 B:HIS250 4.1 16.2 1.0 CG B:HIS250 4.2 15.3 1.0 C08 B:N8Q305 4.2 38.1 1.0 CB B:ASP124 4.3 14.1 1.0 C07 B:N8Q305 4.3 37.5 1.0 OG B:SER249 4.4 15.6 1.0 CA B:CYS208 4.4 13.6 1.0 ZN B:ZN301 4.5 20.3 1.0 C12 B:N8Q305 4.5 30.5 1.0 CE1 B:HIS120 4.6 16.0 1.0 N05 B:N8Q305 4.7 32.3 1.0 NE2 B:HIS189 4.8 16.8 1.0 NE2 B:HIS120 4.9 15.3 1.0 CE B:LYS125 4.9 14.2 1.0

F.Spyrakis, M.Santucci, L.Maso, S.Cross, E.Gianquinto, F.Sannio, F.Verdirosa, F.De Luca, J.D.Docquier, L.Cendron, D.Tondi, A.Venturelli, G.Cruciani, M.P.Costi. Virtual Screening Identifies Broad-Spectrum Beta-Lactamase Inhibitors with Activity on Clinically Relevant Serine- and Metallo-Carbapenemases. Sci Rep V. 10 12763 2020.
ISSN: ESSN 2045-2322
PubMed: 32728062
DOI: 10.1038/S41598-020-69431-Y