Zinc in PDB 5m2k: Crystal Structure of Vancomycin-Zn(II) Complex

The structure of Crystal Structure of Vancomycin-Zn(II) Complex, PDB code: 5m2k was solved by A.Zarkan, H.-R.Macklyne, D.Y.Chirgadze, A.D.Bond, A.R.Hesketh, H.-J.Hong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.13 / 1.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	35.899, 35.899, 55.553, 90.00, 90.00, 120.00
R / Rfree (%)	9.7 / 10.5

The structure of Crystal Structure of Vancomycin-Zn(II) Complex also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Vancomycin-Zn(II) Complex (pdb code 5m2k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Vancomycin-Zn(II) Complex, PDB code: 5m2k:

Zinc binding site 1 out of 1 in the Crystal Structure of Vancomycin-Zn(II) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Vancomycin-Zn(II) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:3.7 occ:1.00 O A:HOH209 2.1 5.2 1.0 O B:HOH221 2.1 5.2 1.0 N B:MLU1 2.1 4.0 1.0 O B:MLU1 2.2 4.1 1.0 C B:MLU1 2.8 3.8 1.0 CA B:MLU1 3.0 4.8 1.0 CN B:MLU1 3.1 5.0 1.0 CB B:MLU1 3.9 6.6 1.0 N B:OMZ2 4.1 4.5 1.0 O1 A:EDO103 4.1 5.1 1.0 O A:HOH224 4.4 13.4 1.0 O A:HOH207 4.5 4.7 1.0 O B:HOH231 4.5 13.4 1.0 CA B:OMZ2 4.8 4.4 1.0 O A:HOH225 4.8 4.7 0.3 CG B:MLU1 5.0 10.1 1.0

A.Zarkan, H.R.Macklyne, D.Y.Chirgadze, A.D.Bond, A.R.Hesketh, H.J.Hong. Zn(II) Mediates Vancomycin Polymerization and Potentiates Its Antibiotic Activity Against Resistant Bacteria. Sci Rep V. 7 4893 2017.
ISSN: ESSN 2045-2322
PubMed: 28687742
DOI: 10.1038/S41598-017-04868-2