Chlorine 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:

Zinc

(Zn)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Vancomycin-Zn(II) Complex (pdb code 5m2k). 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) Complex, PDB code: 5m2k:
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) 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) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:6.0 occ:0.70 CL A:OMZ2 0.0 6.0 0.7 CE1 A:OMZ2 1.7 5.0 1.0 CZ A:OMZ2 2.6 5.6 1.0 CD1 A:OMZ2 2.7 5.0 1.0 OH A:OMZ2 2.9 6.6 1.0 ODE B:OMY6 3.3 4.7 1.0 C5 A:GHP4 3.3 4.5 1.0 C6 A:GHP4 3.6 4.3 1.0 C2 B:EDO104 3.7 6.9 1.0 O6 A:BGC101 3.9 7.4 1.0 CD2 B:OMY6 4.0 4.0 1.0 CE2 A:OMZ2 4.0 6.2 1.0 O5 A:BGC101 4.0 5.3 1.0 CG A:OMZ2 4.1 4.6 1.0 C4 A:GHP4 4.2 4.3 1.0 O2 B:EDO104 4.4 5.0 1.0 C6 A:BGC101 4.4 6.8 1.0 CB B:OMY6 4.4 4.0 1.0 CD2 A:OMZ2 4.5 5.8 1.0 O A:ASN3 4.5 5.9 1.0 CG B:OMY6 4.5 3.9 1.0 C1 B:EDO104 4.6 7.7 1.0 O4 A:GHP4 4.7 4.9 1.0 C1 A:GHP4 4.7 3.8 1.0 O1 B:EDO104 4.7 7.3 1.0 O B:HOH206 4.8 4.9 1.0 C5 A:BGC101 4.9 6.2 1.0 CE2 B:OMY6 5.0 4.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Vancomycin-Zn(II) 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) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:6.2 occ:0.80 CL A:OMY6 0.0 6.2 0.8 CE1 A:OMY6 1.8 5.1 1.0 CD1 A:OMY6 2.7 4.5 1.0 CZ A:OMY6 2.7 4.2 1.0 OCZ A:OMY6 3.0 5.2 1.0 C3 A:GHP4 3.3 4.2 1.0 C2 A:GHP4 3.7 4.2 1.0 C3A A:RER102 3.7 9.5 1.0 C5 A:RER102 3.8 9.3 1.0 C5A A:RER102 3.9 11.3 1.0 C4 A:RER102 4.0 10.3 1.0 C4 A:GHP4 4.0 4.3 1.0 CE2 A:OMY6 4.0 4.3 1.0 CG A:OMY6 4.1 3.8 1.0 O4 A:GHP4 4.4 4.9 1.0 C3 A:RER102 4.5 10.7 1.0 CD2 A:OMY6 4.6 4.2 1.0 C1 A:GHP4 4.6 3.8 1.0 O A:GHP4 4.7 4.6 1.0 C5 A:GHP4 4.9 4.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Vancomycin-Zn(II) 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) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:6.8 occ:0.70 CL B:OMZ2 0.0 6.8 0.7 CE1 B:OMZ2 1.7 5.4 1.0 CZ B:OMZ2 2.6 5.5 1.0 CD1 B:OMZ2 2.7 5.1 1.0 OH B:OMZ2 2.9 6.7 1.0 ODE A:OMY6 3.3 4.7 1.0 C5 B:GHP4 3.3 4.6 1.0 O B:HOH217 3.5 7.7 1.0 C6 B:GHP4 3.6 4.5 1.0 C1 A:EDO103 3.8 6.9 1.0 O6 B:BGC101 3.9 7.6 1.0 CE2 B:OMZ2 4.0 6.2 1.0 CD2 A:OMY6 4.0 4.2 1.0 O5 B:BGC101 4.0 5.4 1.0 CG B:OMZ2 4.1 4.8 1.0 C4 B:GHP4 4.2 4.4 1.0 C6 B:BGC101 4.4 6.8 1.0 O1 A:EDO103 4.4 5.1 1.0 CB A:OMY6 4.4 3.9 1.0 CD2 B:OMZ2 4.5 5.7 1.0 O B:ASN3 4.5 5.7 1.0 CG A:OMY6 4.5 3.8 1.0 C2 A:EDO103 4.6 7.5 1.0 O A:HOH202 4.7 49.0 1.0 O4 B:GHP4 4.7 5.0 1.0 C1 B:GHP4 4.7 3.8 1.0 O2 A:EDO103 4.8 7.2 1.0 O A:HOH207 4.8 4.7 1.0 C5 B:BGC101 4.9 6.5 1.0 CE2 A:OMY6 5.0 4.3 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Vancomycin-Zn(II) 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) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:5.2 occ:0.70 CL B:OMY6 0.0 5.2 0.7 CE1 B:OMY6 1.8 5.1 1.0 CD1 B:OMY6 2.7 4.5 1.0 CZ B:OMY6 2.7 4.3 1.0 OCZ B:OMY6 3.0 5.2 1.0 C3 B:GHP4 3.3 4.4 1.0 C2 B:GHP4 3.7 4.3 1.0 C3A B:RER102 3.7 9.2 1.0 C5 B:RER102 3.8 9.3 1.0 C5A B:RER102 3.9 11.1 1.0 C4 B:RER102 4.0 10.4 1.0 C4 B:GHP4 4.0 4.4 1.0 CE2 B:OMY6 4.0 4.3 1.0 CG B:OMY6 4.1 3.9 1.0 O B:HOH225 4.1 21.0 1.0 O4 B:GHP4 4.4 5.0 1.0 C3 B:RER102 4.5 10.7 1.0 O B:HOH226 4.6 49.2 1.0 CD2 B:OMY6 4.6 4.0 1.0 C1 B:GHP4 4.6 3.8 1.0 O B:GHP4 4.7 4.6 1.0 C5 B:GHP4 4.9 4.6 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