Zinc in PDB 8b20: Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57, PDB code: 8b20 was solved by F.Vascon, L.Lazzarato, M.Bersani, E.Gianquinto, J.D.Docquier, F.Spyrakis, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.31 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.068, 70.444, 73.803, 90, 90, 90
R / Rfree (%)	18.4 / 20.7

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Fluorine	(F)	3 atoms

The binding sites of Zinc atom in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 (pdb code 8b20). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57, PDB code: 8b20:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.4 occ:1.00 ND1 A:HIS122 1.8 20.1 1.0 N3 A:OQK306 2.0 26.9 0.8 NE2 A:HIS120 2.1 24.6 1.0 NE2 A:HIS189 2.1 23.9 1.0 CE1 A:HIS122 2.8 23.5 1.0 CG A:HIS122 2.8 21.4 1.0 C9 A:OQK306 2.9 23.5 0.8 N4 A:OQK306 3.0 23.7 0.8 CD2 A:HIS189 3.0 18.9 1.0 CD2 A:HIS120 3.1 23.1 1.0 CE1 A:HIS120 3.1 24.4 1.0 CE1 A:HIS189 3.1 22.1 1.0 CB A:HIS122 3.3 20.8 1.0 S1 A:OQK306 3.5 27.9 0.8 NE2 A:HIS122 3.9 25.4 1.0 CD2 A:HIS122 3.9 25.1 1.0 C10 A:OQK306 4.1 25.1 0.8 N2 A:OQK306 4.1 25.8 0.8 OD1 A:ASP124 4.2 24.0 1.0 ND1 A:HIS120 4.2 25.4 1.0 CG A:HIS189 4.2 21.7 1.0 ND1 A:HIS189 4.2 21.7 1.0 CG A:HIS120 4.2 21.6 1.0 CG2 A:THR190 4.3 21.3 1.0 ZN A:ZN302 4.5 26.3 1.0 CA A:HIS122 4.7 21.6 1.0 CB A:CYS208 4.8 22.1 1.0 SG A:CYS208 4.8 27.5 1.0

Zinc binding site 2 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:26.3 occ:1.00 OD2 A:ASP124 2.0 28.7 1.0 S1 A:OQK306 2.0 27.9 0.8 NE2 A:HIS250 2.1 24.1 1.0 SG A:CYS208 2.3 27.5 1.0 C9 A:OQK306 2.9 23.5 0.8 CG A:ASP124 3.0 23.9 1.0 CE1 A:HIS250 3.0 26.1 1.0 CD2 A:HIS250 3.2 25.3 1.0 CB A:CYS208 3.4 22.1 1.0 OD1 A:ASP124 3.4 24.0 1.0 N2 A:OQK306 3.6 25.8 0.8 N1 A:OQK306 3.7 29.9 0.8 N3 A:OQK306 3.8 26.9 0.8 CB A:SER249 4.1 25.0 1.0 ND1 A:HIS250 4.2 26.1 1.0 C8 A:OQK306 4.2 33.2 0.8 CG A:HIS250 4.2 25.8 1.0 CB A:ASP124 4.3 22.4 1.0 CE1 A:HIS120 4.4 24.4 1.0 OG A:SER249 4.4 25.4 1.0 CA A:CYS208 4.4 21.7 1.0 ZN A:ZN301 4.5 26.4 1.0 C10 A:OQK306 4.6 25.1 0.8 CE A:LYS125 4.7 25.5 1.0 N4 A:OQK306 4.8 23.7 0.8 C7 A:OQK306 4.8 36.7 0.8 NE2 A:HIS120 4.9 24.6 1.0

Zinc binding site 3 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.9 occ:1.00 ND1 B:HIS122 1.9 22.4 1.0 NE2 B:HIS120 2.0 18.5 1.0 NE2 B:HIS189 2.1 22.9 1.0 CE1 B:HIS122 2.9 24.6 1.0 CD2 B:HIS120 2.9 21.1 1.0 CG B:HIS122 2.9 20.5 1.0 CD2 B:HIS189 2.9 20.5 1.0 CE1 B:HIS120 3.0 20.0 1.0 CE1 B:HIS189 3.2 24.8 1.0 CB B:HIS122 3.3 19.5 1.0 OD1 B:ASP124 3.9 22.4 1.0 NE2 B:HIS122 4.0 22.6 1.0 ZN B:ZN302 4.0 23.8 1.0 CD2 B:HIS122 4.0 22.1 1.0 ND1 B:HIS120 4.1 21.1 1.0 CG B:HIS120 4.1 19.9 1.0 CG B:HIS189 4.1 18.9 1.0 ND1 B:HIS189 4.2 20.8 1.0 SG B:CYS208 4.3 21.7 1.0 CB B:CYS208 4.3 18.6 1.0 CG2 B:THR190 4.4 22.5 1.0 OD2 B:ASP124 4.7 25.1 1.0 ND2 B:ASN220 4.7 33.2 1.0 CG B:ASP124 4.7 22.8 1.0 CA B:HIS122 4.8 18.6 1.0

Zinc binding site 4 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:23.8 occ:1.00 OD2 B:ASP124 1.9 25.1 1.0 NE2 B:HIS250 2.0 23.0 1.0 SG B:CYS208 2.3 21.7 1.0 CE1 B:HIS250 3.0 26.3 1.0 CG B:ASP124 3.0 22.8 1.0 CD2 B:HIS250 3.1 21.3 1.0 CB B:CYS208 3.3 18.6 1.0 OD1 B:ASP124 3.5 22.4 1.0 ZN B:ZN301 4.0 25.9 1.0 ND1 B:HIS250 4.1 24.9 1.0 CG B:HIS250 4.2 22.5 1.0 CB B:SER249 4.2 21.3 1.0 CB B:ASP124 4.3 19.7 1.0 CA B:CYS208 4.4 19.1 1.0 NE2 B:HIS189 4.6 22.9 1.0 CE1 B:HIS120 4.6 20.0 1.0 OG B:SER249 4.6 20.4 1.0 NE2 B:HIS120 4.7 18.5 1.0 CE1 B:HIS189 4.8 24.8 1.0

F.Vascon, L.Lazzarato, M.Bersani, E.Gianquinto, J.D.Docquier, F.Spyrakis, D.Tondi, L.Cendron. Structural Characterization of Triazole-Based Inhibitors of Metallo-Beta-Lactamases To Be Published.