Calcium 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:

Fluorine	(F)	3 atoms
Zinc	(Zn)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57, PDB code: 8b20:
Jump to Calcium binding site number: 1; 2; 3;

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


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 CP57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:48.3 occ:1.00 OE1 B:GLU227 2.4 55.1 1.0 OD2 A:ASP223 2.4 42.5 1.0 OE1 A:GLU152 2.6 38.5 1.0 OE2 B:GLU227 2.8 58.1 1.0 OE2 A:GLU152 2.8 43.8 1.0 CD B:GLU227 2.9 48.9 1.0 OD1 A:ASP223 3.0 47.4 1.0 CG A:ASP223 3.1 42.9 1.0 CD A:GLU152 3.1 38.6 1.0 NE2 A:HIS122 4.0 25.4 1.0 CG B:GLU227 4.4 39.1 1.0 CB A:ASP223 4.5 34.5 1.0 CD2 A:HIS122 4.6 25.1 1.0 CG A:GLU152 4.6 35.6 1.0 O A:HOH443 4.6 36.8 1.0 NE2 B:HIS228 4.7 28.6 1.0 CE1 B:HIS228 4.7 29.0 1.0 O A:HOH406 4.8 35.1 1.0

Calcium binding site 2 out of 3 in the Ndm-1 Metallo-Beta-Lactamase in Complex with Triazole-Based Inhibitor CP57


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 CP57 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:80.2 occ:1.00 OD2 A:ASP95 2.7 34.1 1.0 OD2 A:ASP130 2.7 40.9 1.0 O A:HOH454 2.7 21.6 1.0 CG A:ASP130 3.7 31.0 1.0 CG A:ASP95 3.7 34.8 1.0 OD1 A:ASP95 4.0 27.3 1.0 CB A:ASP130 4.1 26.9 1.0 O A:HOH452 4.2 31.6 1.0 O A:GLY127 4.5 21.4 1.0 OD1 A:ASP130 4.7 36.6 1.0 O A:HOH419 4.7 21.9 1.0 CG2 A:VAL155 4.8 30.4 1.0

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


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 CP57 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:29.9 occ:1.00 OE1 A:GLU227 2.3 38.5 1.0 OD2 B:ASP223 2.3 33.3 1.0 OE2 B:GLU152 2.4 31.4 1.0 OE1 B:GLU152 2.5 24.3 1.0 O B:HOH469 2.5 43.7 1.0 OE2 A:GLU227 2.7 36.6 1.0 CD B:GLU152 2.7 23.9 1.0 OD1 B:ASP223 2.8 40.4 1.0 CD A:GLU227 2.9 35.1 1.0 CG B:ASP223 2.9 31.6 1.0 O B:HOH426 4.3 29.8 1.0 CG B:GLU152 4.3 23.6 1.0 CG A:GLU227 4.4 33.8 1.0 NE2 A:HIS228 4.4 25.0 1.0 NE2 B:HIS122 4.4 22.6 1.0 CB B:ASP223 4.4 25.7 1.0 CE1 A:HIS228 4.5 24.8 1.0 O B:HOH412 4.6 29.8 1.0 CD2 B:HIS122 4.9 22.1 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.