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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5nbk:

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

Chlorine Binding Sites:

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 5nbk

Go back to Chlorine Binding Sites List in 5nbk
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 5nbk

Go back to Chlorine Binding Sites List in 5nbk
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

Reference:

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
Page generated: Sat Dec 12 12:09:05 2020

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