Chlorine in PDB 5nbk: Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data

All present enzymatic activity of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data:
3.5.2.6;

The structure of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data, PDB code: 5nbk was solved by J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.047, 108.047, 92.571, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.9

The structure of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Chlorine atom in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data (pdb code 5nbk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data, PDB code: 5nbk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:64.7 occ:1.00 N A:ASP95 3.4 39.2 1.0 OD2 A:ASP95 3.7 42.4 1.0 CB A:THR94 3.8 37.9 1.0 CA A:THR94 3.8 36.8 1.0 CG A:ASP95 4.0 40.7 1.0 O A:GLY127 4.0 39.5 1.0 C A:THR94 4.1 36.6 1.0 CB A:ASP95 4.2 40.5 1.0 CG2 A:THR94 4.3 38.9 1.0 CA A:ASP95 4.4 39.3 1.0 OD1 A:ASP95 4.6 40.1 1.0 O A:TRP93 4.9 36.6 1.0

Chlorine binding site 2 out of 2 in the Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ndm-1 Metallo-Beta-Lactamase: A Parsimonious Interpretation of the Diffraction Data within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl305 b:57.9 occ:1.00 NE C:ARG264 3.5 58.3 1.0 CA C:HIS261 3.7 40.8 1.0 ND1 C:HIS261 3.8 44.4 1.0 CB C:HIS261 3.9 40.8 1.0 N C:HIS261 4.1 41.3 1.0 CD C:ARG264 4.1 55.5 1.0 OG1 C:THR260 4.2 46.2 1.0 CG C:HIS261 4.3 41.6 1.0 C C:THR260 4.4 41.7 1.0 O C:THR260 4.4 43.8 1.0 NH2 C:ARG264 4.4 62.1 1.0 CZ C:ARG264 4.5 60.2 1.0 CB C:ARG264 4.8 46.1 1.0 CE1 C:HIS261 4.9 44.2 1.0 C C:HIS261 5.0 39.1 1.0 O C:ALA257 5.0 39.8 1.0

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001