Zinc in PDB 8b1w: Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35, PDB code: 8b1w 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)	36.88 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.19, 73.699, 77.28, 90, 90, 90
R / Rfree (%)	19.2 / 22.2

The structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Bromine	(Br)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35 (pdb code 8b1w). 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 CP35, PDB code: 8b1w:
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 CP35


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 CP35 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.0 occ:1.00 ND1 A:HIS122 2.0 16.4 1.0 NE2 A:HIS189 2.0 18.3 1.0 O A:HOH440 2.1 16.8 1.0 NE2 A:HIS120 2.1 16.7 1.0 CE1 A:HIS122 2.9 17.2 1.0 CD2 A:HIS189 3.0 17.5 1.0 CG A:HIS122 3.0 19.1 1.0 CE1 A:HIS189 3.1 18.8 1.0 CD2 A:HIS120 3.1 15.8 1.0 CE1 A:HIS120 3.1 17.9 1.0 CB A:HIS122 3.4 17.4 1.0 ZN A:ZN302 3.4 23.4 1.0 SG A:CYS208 3.9 19.6 1.0 OD1 A:ASP124 4.0 19.5 1.0 CB A:CYS208 4.1 20.4 1.0 NE2 A:HIS122 4.1 18.7 1.0 CD2 A:HIS122 4.1 17.9 1.0 ND1 A:HIS189 4.1 17.1 1.0 CG A:HIS189 4.2 15.6 1.0 ND1 A:HIS120 4.2 16.5 1.0 CG A:HIS120 4.2 17.5 1.0 CG2 A:THR190 4.5 15.9 1.0 OD2 A:ASP124 4.6 21.8 1.0 CG A:ASP124 4.7 20.8 1.0 CA A:HIS122 4.8 17.9 1.0 C10 A:OQU305 4.9 30.5 0.8 S1 A:OQU305 5.0 24.9 0.8

Zinc binding site 2 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.4 occ:1.00 O A:HOH440 2.0 16.8 1.0 OD2 A:ASP124 2.1 21.8 1.0 NE2 A:HIS250 2.1 20.9 1.0 SG A:CYS208 2.2 19.6 1.0 CG A:ASP124 3.0 20.8 1.0 CE1 A:HIS250 3.0 20.2 1.0 CD2 A:HIS250 3.1 20.3 1.0 OD1 A:ASP124 3.3 19.5 1.0 CB A:CYS208 3.4 20.4 1.0 ZN A:ZN301 3.4 20.0 1.0 S1 A:OQU305 4.0 24.9 0.8 C4 A:OQU305 4.1 34.6 0.8 ND1 A:HIS250 4.2 22.2 1.0 CB A:SER249 4.2 15.8 1.0 CG A:HIS250 4.2 22.2 1.0 C10 A:OQU305 4.2 30.5 0.8 NE2 A:HIS189 4.3 18.3 1.0 NE2 A:HIS120 4.4 16.7 1.0 CB A:ASP124 4.4 19.8 1.0 CE1 A:HIS120 4.4 17.9 1.0 OG A:SER249 4.5 18.6 1.0 CA A:CYS208 4.6 17.8 1.0 C5 A:OQU305 4.6 33.0 0.8 CE1 A:HIS189 4.6 18.8 1.0 CD A:LYS125 4.8 20.3 1.0 C3 A:OQU305 4.8 27.2 0.8 CE A:LYS125 4.8 19.6 1.0 CG A:LYS125 4.9 20.5 1.0

Zinc binding site 3 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.4 occ:1.00 O B:HOH434 1.8 19.6 1.0 NE2 B:HIS189 2.0 17.3 1.0 NE2 B:HIS120 2.0 17.5 1.0 ND1 B:HIS122 2.1 16.6 1.0 CD2 B:HIS189 3.0 15.3 1.0 CE1 B:HIS120 3.0 17.9 1.0 CD2 B:HIS120 3.0 17.1 1.0 CE1 B:HIS122 3.1 16.2 1.0 CE1 B:HIS189 3.1 17.1 1.0 CG B:HIS122 3.1 17.4 1.0 CB B:HIS122 3.4 14.3 1.0 ZN B:ZN302 3.5 22.7 1.0 SG B:CYS208 3.9 18.2 1.0 OD1 B:ASP124 3.9 18.2 1.0 ND1 B:HIS120 4.1 17.0 1.0 ND1 B:HIS189 4.1 15.2 1.0 CG B:HIS189 4.2 15.7 1.0 CG B:HIS120 4.2 16.9 1.0 CB B:CYS208 4.2 17.2 1.0 NE2 B:HIS122 4.2 17.4 1.0 CD2 B:HIS122 4.2 17.1 1.0 OD2 B:ASP124 4.5 22.4 1.0 CG2 B:THR190 4.5 17.1 1.0 CG B:ASP124 4.6 19.8 1.0 CA B:HIS122 4.9 15.2 1.0 C10 B:OQU305 4.9 37.8 0.8 S1 B:OQU305 4.9 30.5 0.8

Zinc binding site 4 out of 4 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35


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 CP35 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.7 occ:1.00 OD2 B:ASP124 1.9 22.4 1.0 NE2 B:HIS250 2.0 17.3 1.0 O B:HOH434 2.1 19.6 1.0 SG B:CYS208 2.3 18.2 1.0 CG B:ASP124 2.9 19.8 1.0 CE1 B:HIS250 3.0 17.7 1.0 CD2 B:HIS250 3.1 17.5 1.0 OD1 B:ASP124 3.3 18.2 1.0 CB B:CYS208 3.4 17.2 1.0 ZN B:ZN301 3.5 19.4 1.0 C4 B:OQU305 3.9 32.6 0.8 S1 B:OQU305 4.0 30.5 0.8 ND1 B:HIS250 4.1 19.6 1.0 CG B:HIS250 4.2 16.8 1.0 CB B:SER249 4.2 19.8 1.0 C10 B:OQU305 4.2 37.8 0.8 CB B:ASP124 4.2 16.1 1.0 NE2 B:HIS189 4.2 17.3 1.0 NE2 B:HIS120 4.4 17.5 1.0 CE1 B:HIS120 4.5 17.9 1.0 C5 B:OQU305 4.5 36.5 0.8 OG B:SER249 4.6 19.6 1.0 CE1 B:HIS189 4.6 17.1 1.0 CA B:CYS208 4.6 18.4 1.0 C3 B:OQU305 4.7 29.5 0.8 CE B:LYS125 4.8 21.0 1.0 N4 B:OQU305 4.9 29.1 0.8 CD B:LYS125 4.9 17.6 1.0 CG B:LYS125 5.0 17.5 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.