Zinc in PDB 8b1z: Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56, PDB code: 8b1z 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)	34.19 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.61, 73.964, 77.115, 90, 90, 90
R / Rfree (%)	17.3 / 20.9

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Fluorine	(F)	6 atoms

The binding sites of Zinc atom in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56 (pdb code 8b1z). 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 CP56, PDB code: 8b1z:
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 CP56


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 CP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.1 occ:0.94 ND1 A:HIS122 2.0 21.8 1.0 N3 A:ORL304 2.0 13.8 0.7 NE2 A:HIS189 2.0 20.0 1.0 NE2 A:HIS120 2.1 18.9 1.0 C8 A:ORL304 2.9 15.9 0.7 CG A:HIS122 2.9 20.1 1.0 CE1 A:HIS122 3.0 23.2 1.0 CE1 A:HIS189 3.0 22.2 1.0 N4 A:ORL304 3.0 16.1 0.7 CD2 A:HIS120 3.0 19.2 1.0 CD2 A:HIS189 3.0 19.8 1.0 CE1 A:HIS120 3.1 20.3 1.0 CB A:HIS122 3.2 17.8 1.0 S1 A:ORL304 3.5 16.9 0.7 C9 A:ORL304 4.1 16.6 0.7 ND1 A:HIS189 4.1 20.0 1.0 CD2 A:HIS122 4.1 22.8 1.0 NE2 A:HIS122 4.1 23.3 1.0 N2 A:ORL304 4.1 17.0 0.7 CG A:HIS189 4.2 18.9 1.0 CG A:HIS120 4.2 17.9 1.0 ND1 A:HIS120 4.2 19.4 1.0 OD1 A:ASP124 4.3 21.6 1.0 CG2 A:THR190 4.4 20.2 1.0 O A:HOH470 4.5 37.4 1.0 ZN A:ZN302 4.6 19.5 0.9 CA A:HIS122 4.7 16.9 1.0

Zinc binding site 2 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


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 CP56 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.5 occ:0.95 OD2 A:ASP124 1.9 22.4 1.0 NE2 A:HIS250 2.1 20.1 1.0 SG A:CYS208 2.3 20.3 1.0 S1 A:ORL304 2.3 16.9 0.7 C8 A:ORL304 3.0 15.9 0.7 CG A:ASP124 3.0 21.6 1.0 CE1 A:HIS250 3.1 20.5 1.0 CD2 A:HIS250 3.1 21.9 1.0 CB A:CYS208 3.3 19.2 1.0 OD1 A:ASP124 3.5 21.6 1.0 N2 A:ORL304 3.6 17.0 0.7 N1 A:ORL304 3.7 21.5 0.7 N3 A:ORL304 3.8 13.8 0.7 C7 A:ORL304 3.9 23.9 0.7 CB A:SER249 4.1 20.5 1.0 ND1 A:HIS250 4.2 19.9 1.0 CE1 A:HIS120 4.2 20.3 1.0 CG A:HIS250 4.2 19.6 1.0 CB A:ASP124 4.2 19.5 1.0 CA A:CYS208 4.4 19.1 1.0 OG A:SER249 4.4 23.4 1.0 C9 A:ORL304 4.5 16.6 0.7 ZN A:ZN301 4.6 20.1 0.9 N4 A:ORL304 4.7 16.1 0.7 NE2 A:HIS120 4.7 18.9 1.0 CE A:LYS125 4.9 23.9 1.0 C6 A:ORL304 4.9 29.1 0.7

Zinc binding site 3 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


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 CP56 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.2 occ:1.00 N3 B:ORL303 2.0 18.5 0.8 ND1 B:HIS122 2.0 22.7 1.0 NE2 B:HIS120 2.1 17.1 1.0 NE2 B:HIS189 2.1 16.6 1.0 C8 B:ORL303 2.9 20.5 0.8 CD2 B:HIS120 3.0 17.6 1.0 N4 B:ORL303 3.0 21.3 0.8 CG B:HIS122 3.0 19.2 1.0 CE1 B:HIS122 3.0 19.0 1.0 CD2 B:HIS189 3.0 18.8 1.0 CE1 B:HIS120 3.1 19.2 1.0 CE1 B:HIS189 3.1 19.5 1.0 CB B:HIS122 3.3 18.6 1.0 S1 B:ORL303 3.4 19.1 0.8 C9 B:ORL303 4.1 18.7 0.8 ND1 B:HIS120 4.1 19.4 1.0 N2 B:ORL303 4.1 20.8 0.8 CG B:HIS120 4.1 16.8 1.0 NE2 B:HIS122 4.2 24.5 1.0 CD2 B:HIS122 4.2 21.1 1.0 ND1 B:HIS189 4.2 20.9 1.0 CG B:HIS189 4.2 19.7 1.0 OD1 B:ASP124 4.3 19.9 1.0 CG2 B:THR190 4.3 19.9 1.0 ZN B:ZN302 4.6 19.3 1.0 CA B:HIS122 4.7 16.0 1.0

Zinc binding site 4 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP56


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 CP56 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:19.3 occ:1.00 OD2 B:ASP124 1.9 17.7 1.0 NE2 B:HIS250 2.1 17.8 1.0 SG B:CYS208 2.2 19.1 1.0 S1 B:ORL303 2.3 19.1 0.8 CG B:ASP124 3.0 19.7 1.0 C8 B:ORL303 3.0 20.5 0.8 CE1 B:HIS250 3.1 19.9 1.0 CD2 B:HIS250 3.1 16.5 1.0 CB B:CYS208 3.2 16.8 1.0 OD1 B:ASP124 3.4 19.9 1.0 N2 B:ORL303 3.6 20.8 0.8 N1 B:ORL303 3.7 26.1 0.8 N3 B:ORL303 3.9 18.5 0.8 CB B:SER249 4.1 17.0 1.0 C7 B:ORL303 4.1 27.8 0.8 ND1 B:HIS250 4.2 16.9 1.0 CG B:HIS250 4.2 17.3 1.0 CE1 B:HIS120 4.2 19.2 1.0 CB B:ASP124 4.2 17.9 1.0 CA B:CYS208 4.4 16.9 1.0 OG B:SER249 4.5 20.4 1.0 ZN B:ZN301 4.6 21.2 1.0 C9 B:ORL303 4.6 18.7 0.8 C6 B:ORL303 4.6 31.1 0.8 CE B:LYS125 4.7 19.7 1.0 N4 B:ORL303 4.8 21.3 0.8 NE2 B:HIS120 4.8 17.1 1.0 NZ B:LYS211 4.9 29.1 1.0 C5 B:ORL303 5.0 38.1 0.8

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.