Chlorine in PDB 5ypk: Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk was solved by H.Feng, D.Wang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.21 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.240, 73.610, 154.520, 90.00, 90.08, 90.00
R / Rfree (%)	18.6 / 22.9

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex also contains other interesting chemical elements:

Zinc	(Zn)	16 atoms
Sodium	(Na)	7 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex (pdb code 5ypk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk:

Chlorine binding site 1 out of 1 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl305 b:46.8 occ:1.00 O D:HOH547 2.1 45.3 1.0 O G:HOH452 2.7 36.8 1.0 N D:SER160 3.0 14.1 1.0 O D:HOH440 3.1 32.3 1.0 O G:HOH519 3.2 37.7 1.0 CA D:HIS159 3.6 18.6 1.0 O D:HOH518 3.6 28.5 1.0 C D:HIS159 3.8 20.1 1.0 CB D:SER160 3.9 19.5 1.0 CA D:SER160 3.9 16.1 1.0 NH1 G:ARG264 4.0 60.8 1.0 O G:HOH441 4.0 38.5 1.0 CB D:HIS159 4.1 20.3 1.0 O D:SER160 4.2 16.8 1.0 OG D:SER160 4.3 18.9 1.0 ND1 D:HIS159 4.4 23.3 1.0 O D:GLN158 4.4 25.2 1.0 O D:HOH425 4.5 28.1 1.0 C D:SER160 4.6 16.7 1.0 O D:HOH575 4.7 34.6 1.0 CG D:HIS159 4.7 22.6 1.0 N D:HIS159 4.8 15.6 1.0 O F:HOH572 4.9 33.9 1.0 CZ G:ARG264 4.9 55.4 1.0 O D:HIS159 5.0 11.9 1.0

H.Feng, X.Liu, S.Wang, J.Fleming, D.C.Wang, W.Liu. The Mechanism of Ndm-1-Catalyzed Carbapenem Hydrolysis Is Distinct From That of Penicillin or Cephalosporin Hydrolysis. Nat Commun V. 8 2242 2017.
ISSN: ESSN 2041-1723
PubMed: 29269938
DOI: 10.1038/S41467-017-02339-W