Calcium 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:

Zinc	(Zn)	4 atoms
Fluorine	(F)	6 atoms
Bromine	(Br)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP35, PDB code: 8b1w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca303 b:23.9 occ:1.00 OD2 A:ASP223 2.3 21.7 1.0 O A:HOH468 2.4 31.3 1.0 O B:HOH424 2.4 25.5 1.0 O A:HOH467 2.4 38.0 1.0 OD1 A:ASP223 2.6 26.2 1.0 OE1 A:GLU152 2.6 24.0 1.0 OE2 A:GLU152 2.6 23.8 1.0 CG A:ASP223 2.8 25.0 1.0 CD A:GLU152 3.0 24.8 1.0 CB A:ASP223 4.3 21.2 1.0 OE1 B:GLU227 4.3 41.8 1.0 NE2 B:HIS228 4.5 26.0 1.0 CG A:GLU152 4.5 21.4 1.0 NE2 A:HIS122 4.6 18.7 1.0 CE1 B:HIS228 4.6 23.8 1.0 O A:HOH431 4.7 22.5 1.0 CD2 A:HIS122 5.0 17.9 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:46.1 occ:1.00 O A:HOH459 2.4 20.3 1.0 OD2 A:ASP95 2.5 21.6 1.0 OD2 A:ASP130 2.5 24.7 1.0 O A:HOH407 2.6 26.9 1.0 CG A:ASP130 3.3 22.9 1.0 CG A:ASP95 3.5 25.2 1.0 CB A:ASP130 3.7 21.6 1.0 OD1 A:ASP95 3.8 23.6 1.0 O A:GLY127 4.2 18.7 1.0 O A:HOH433 4.3 28.3 1.0 O A:HOH460 4.3 24.1 1.0 OD1 A:ASP130 4.3 26.2 1.0 O A:HOH424 4.5 16.9 1.0 CG2 A:VAL155 4.7 20.6 1.0 N A:ASP130 4.7 19.2 1.0 CA A:ASP130 4.8 21.2 1.0 CB A:ASP95 4.8 20.7 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca303 b:66.8 occ:1.00 OD2 B:ASP95 2.4 28.0 1.0 O B:HOH468 2.6 25.4 1.0 OD2 B:ASP130 2.6 26.9 1.0 CG B:ASP130 3.3 23.7 1.0 CG B:ASP95 3.3 27.8 1.0 OD1 B:ASP95 3.6 27.0 1.0 CB B:ASP130 3.6 19.8 1.0 O B:HOH403 3.9 22.8 1.0 OD1 B:ASP130 4.3 27.4 1.0 O B:HOH450 4.3 26.1 1.0 O B:GLY127 4.5 17.8 1.0 N B:ASP130 4.6 18.2 1.0 CG2 B:VAL155 4.6 17.1 1.0 CA B:ASP130 4.7 17.9 1.0 CB B:ASP95 4.7 22.1 1.0 O B:HOH449 4.8 18.7 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:24.0 occ:1.00 OD2 B:ASP223 2.4 27.7 1.0 O A:HOH404 2.4 31.0 1.0 O B:HOH465 2.5 32.6 1.0 OE2 B:GLU152 2.5 23.4 1.0 OE1 B:GLU152 2.5 20.8 1.0 OE2 A:GLU227 2.6 32.0 1.0 OD1 B:ASP223 2.6 29.2 1.0 CD B:GLU152 2.8 22.6 1.0 CG B:ASP223 2.9 28.2 1.0 OE1 A:GLU227 2.9 47.6 1.0 CD A:GLU227 3.0 35.4 1.0 CG B:GLU152 4.3 20.2 1.0 O1 B:EDO307 4.3 40.4 1.0 CB B:ASP223 4.4 23.1 1.0 NE2 B:HIS122 4.4 17.4 1.0 NE2 A:HIS228 4.5 21.3 1.0 CG A:GLU227 4.5 29.4 1.0 O B:HOH410 4.6 25.6 1.0 CE1 A:HIS228 4.8 19.5 1.0 CD2 B:HIS122 4.9 17.1 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.