Chlorine in PDB 5m2h: Crystal Structure of Vancomycin-Zn(II)-Citrate Complex

The structure of Crystal Structure of Vancomycin-Zn(II)-Citrate Complex, PDB code: 5m2h 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)	37.31 / 0.95
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.038, 57.481, 21.638, 90.00, 90.00, 90.00
R / Rfree (%)	10.5 / 11.8

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

Zinc

(Zn)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Vancomycin-Zn(II)-Citrate Complex (pdb code 5m2h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Vancomycin-Zn(II)-Citrate Complex, PDB code: 5m2h:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Vancomycin-Zn(II)-Citrate 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 Vancomycin-Zn(II)-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:5.2 occ:1.00 CL A:OMZ2 0.0 5.2 1.0 CE1 A:OMZ2 1.7 4.3 1.0 CD1 A:OMZ2 2.7 4.3 1.0 CZ A:OMZ2 2.7 3.8 1.0 OH A:OMZ2 3.0 4.3 1.0 C5 A:GHP4 3.4 2.9 1.0 C6 A:GHP4 3.5 3.0 1.0 CD2 B:OMY6 3.6 3.1 1.0 CE2 B:OMY6 3.9 3.3 1.0 CG A:OMZ2 4.0 4.2 1.0 CE2 A:OMZ2 4.0 4.1 1.0 C4 A:GHP4 4.3 2.9 1.0 O5 A:BGC101 4.3 3.1 1.0 ODE B:OMY6 4.4 4.3 1.0 O6 A:BGC101 4.5 7.9 1.0 CD2 A:OMZ2 4.5 4.4 1.0 C1 A:GHP4 4.6 2.7 1.0 CG B:OMY6 4.6 3.1 1.0 C6 A:BGC101 4.7 4.9 1.0 O A:ASN3 4.7 5.8 1.0 O4 A:GHP4 4.9 3.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Vancomycin-Zn(II)-Citrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Vancomycin-Zn(II)-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:5.8 occ:1.00 CL A:OMY6 0.0 5.8 1.0 CE1 A:OMY6 1.7 4.0 1.0 CD1 A:OMY6 2.7 3.8 1.0 CZ A:OMY6 2.8 3.3 1.0 OCZ A:OMY6 3.1 3.9 1.0 C3 A:GHP4 3.2 2.9 1.0 O5 A:CIT104 3.3 6.1 1.0 C2 A:GHP4 3.5 3.0 1.0 C5 A:RER102 3.7 4.0 1.0 O A:HOH220 3.7 16.2 1.0 C4 A:GHP4 3.8 2.9 1.0 C5A A:RER102 3.8 4.8 1.0 C3A A:RER102 3.9 5.7 1.0 C4 A:RER102 3.9 4.6 1.0 C4 A:CIT104 4.0 5.3 1.0 CG A:OMY6 4.0 3.5 1.0 O A:HOH241 4.0 16.5 1.0 CE2 A:OMY6 4.1 3.8 1.0 O4 A:GHP4 4.2 3.2 1.0 C6 A:CIT104 4.2 5.0 1.0 C2 A:CIT104 4.3 4.8 1.0 C1 A:GHP4 4.3 2.7 1.0 C3 A:CIT104 4.4 4.5 1.0 C5 A:GHP4 4.5 2.9 1.0 CD2 A:OMY6 4.6 3.9 1.0 C3 A:RER102 4.6 5.0 1.0 O A:HOH232 4.6 14.7 1.0 O A:GHP4 4.7 3.5 1.0 C6 A:GHP4 4.7 3.0 1.0 O A:HOH213 4.8 7.0 1.0 O B:HOH224 4.8 10.1 1.0 C A:GHP4 4.9 2.8 1.0 C5 A:CIT104 5.0 6.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Vancomycin-Zn(II)-Citrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Vancomycin-Zn(II)-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:5.9 occ:0.70 CL B:OMZ2 0.0 5.9 0.7 CE1 B:OMZ2 1.7 3.8 1.0 CZ B:OMZ2 2.7 3.5 1.0 CD1 B:OMZ2 2.7 3.8 1.0 OH B:OMZ2 3.0 3.9 1.0 C5 B:GHP4 3.3 3.4 1.0 O A:HOH233 3.5 16.6 0.5 C6 B:GHP4 3.5 3.1 1.0 O A:HOH227 3.5 40.9 1.0 CD2 A:OMY6 3.6 3.9 1.0 O A:HOH207 3.8 11.5 1.0 CE2 A:OMY6 3.8 3.8 1.0 C3A B:RER102 3.9 5.2 1.0 C5 B:RER102 3.9 3.8 1.0 CE2 B:OMZ2 4.0 3.9 1.0 C4 B:RER102 4.0 4.9 1.0 CG B:OMZ2 4.0 3.5 1.0 C5A B:RER102 4.1 4.9 1.0 C4 B:GHP4 4.3 3.3 1.0 O B:HOH224 4.4 10.1 1.0 C1 B:GHP4 4.5 3.0 1.0 CD2 B:OMZ2 4.5 3.7 1.0 C3 B:RER102 4.6 4.9 1.0 CG A:OMY6 4.6 3.5 1.0 ODE A:OMY6 4.7 4.6 1.0 O4 B:GHP4 4.8 3.4 1.0 O B:ASN3 4.9 4.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Vancomycin-Zn(II)-Citrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Vancomycin-Zn(II)-Citrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:5.5 occ:1.00 CL B:OMY6 0.0 5.5 1.0 CE1 B:OMY6 1.7 3.7 1.0 CD1 B:OMY6 2.7 3.4 1.0 CZ B:OMY6 2.8 3.2 1.0 OCZ B:OMY6 3.1 3.7 1.0 C3 B:GHP4 3.1 3.4 1.0 O5 B:BGC101 3.4 4.8 1.0 C2 B:GHP4 3.4 3.2 1.0 C6 B:BGC101 3.7 7.1 1.0 C4 B:GHP4 3.8 3.3 1.0 O B:HOH208 3.9 7.5 1.0 C5 B:BGC101 3.9 5.4 1.0 CG B:OMY6 4.0 3.1 1.0 CE2 B:OMY6 4.1 3.3 1.0 C1 B:GHP4 4.2 3.0 1.0 C1 B:BGC101 4.2 3.6 1.0 O B:GHP4 4.2 3.7 1.0 O4 B:GHP4 4.4 3.4 1.0 O6 B:BGC101 4.4 9.3 1.0 C5 B:GHP4 4.5 3.4 1.0 CD2 B:OMY6 4.6 3.1 1.0 C B:GHP4 4.6 2.7 1.0 C6 B:GHP4 4.6 3.1 1.0 O B:HOH218 4.6 6.2 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