Chlorine in PDB 1c0q: Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid

The structure of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid, PDB code: 1c0q was solved by P.J.Loll, J.Kaplan, B.Selinsky, P.H.Axelsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	28.400, 28.400, 65.730, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 13.9

The binding sites of Chlorine atom in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid (pdb code 1c0q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid, PDB code: 1c0q:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:7.8 occ:1.00 CL A:OMZ2 0.0 7.8 1.0 CE1 A:OMZ2 1.7 4.9 1.0 CD1 A:OMZ2 2.7 4.6 1.0 CZ A:OMZ2 2.7 4.8 1.0 OH A:OMZ2 3.0 5.5 1.0 C5 A:GHP4 3.4 4.6 1.0 CD2 B:OMY6 3.4 4.9 1.0 C6 A:GHP4 3.6 4.0 1.0 O B:HOH2008 3.7 15.1 1.0 O A:HOH2022 3.8 14.1 0.3 CE2 B:OMY6 3.9 5.9 1.0 CE2 A:OMZ2 4.0 4.9 1.0 CG A:OMZ2 4.0 4.2 1.0 ODE B:OMY6 4.0 4.9 1.0 O5 A:BGC8 4.2 6.9 1.0 C6 A:BGC8 4.2 11.7 1.0 O6 A:BGC8 4.3 13.3 1.0 C4 A:GHP4 4.4 4.4 1.0 CG B:OMY6 4.4 5.0 1.0 CD2 A:OMZ2 4.5 4.4 1.0 C1 A:GHP4 4.7 3.6 1.0 O A:ASN3 4.7 3.8 1.0 CB B:OMY6 4.8 4.8 1.0 C5 A:BGC8 4.9 9.7 1.0 O4 A:GHP4 4.9 5.0 1.0 O A:HOH2007 5.0 14.8 0.7

Chlorine binding site 2 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:5.6 occ:1.00 CL A:OMY6 0.0 5.6 1.0 CE1 A:OMY6 1.7 4.4 1.0 CD1 A:OMY6 2.7 4.0 1.0 CZ A:OMY6 2.7 4.2 1.0 OCZ A:OMY6 3.0 4.8 1.0 C3 A:GHP4 3.2 4.3 1.0 C2 A:GHP4 3.5 4.1 1.0 C3A A:RER9 3.7 8.4 1.0 C5 A:RER9 3.8 10.2 1.0 C4 A:GHP4 3.9 4.4 1.0 CE2 A:OMY6 4.0 4.2 1.0 CG A:OMY6 4.0 3.9 1.0 C4 A:RER9 4.0 11.0 1.0 C5A A:RER9 4.1 12.6 1.0 O A:HOH2002 4.2 7.5 1.0 C1 A:GHP4 4.3 3.6 1.0 O4 A:GHP4 4.3 5.0 1.0 C3 A:RER9 4.5 8.9 1.0 CD2 A:OMY6 4.5 3.9 1.0 O A:GHP4 4.6 3.6 1.0 C5 A:GHP4 4.6 4.6 1.0 C6 A:GHP4 4.8 4.0 1.0 C A:GHP4 4.8 3.3 1.0 CL A:CL21 4.9 5.4 1.0

Chlorine binding site 3 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:5.4 occ:1.00 CL B:OMZ2 0.0 5.4 1.0 CE1 B:OMZ2 1.7 4.5 1.0 CD1 B:OMZ2 2.7 4.8 1.0 CZ B:OMZ2 2.7 4.9 1.0 OH B:OMZ2 3.0 5.4 1.0 C5 B:GHP4 3.4 5.0 1.0 C6 B:GHP4 3.5 4.7 1.0 C5 B:RER9 3.9 6.0 1.0 C4 B:RER9 4.0 4.8 1.0 CD2 A:OMY6 4.0 3.9 1.0 O B:HOH2001 4.0 9.8 1.0 C5A B:RER9 4.0 7.0 1.0 CE2 B:OMZ2 4.0 6.1 1.0 CG B:OMZ2 4.0 5.5 1.0 C3A B:RER9 4.2 4.7 1.0 CE2 A:OMY6 4.2 4.2 1.0 CD2 B:OMZ2 4.5 6.3 1.0 C4 B:GHP4 4.5 6.4 1.0 C1 B:GHP4 4.6 4.3 1.0 C3 B:RER9 4.7 4.4 1.0 O B:ASN3 4.7 5.8 1.0 ODE A:OMY6 4.8 4.8 1.0 O B:OMZ2 4.9 5.9 1.0 C B:ASN3 4.9 4.5 1.0 O4 B:GHP4 5.0 5.3 0.6

Chlorine binding site 4 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:9.5 occ:1.00 CL B:OMY6 0.0 9.5 1.0 CE1 B:OMY6 1.7 6.7 1.0 CD1 B:OMY6 2.7 5.7 1.0 CZ B:OMY6 2.7 6.2 1.0 OCZ B:OMY6 3.0 8.4 1.0 C3 B:GHP4 3.1 6.4 1.0 O5 B:BGC8 3.2 5.8 0.4 O6 B:BGC8 3.3 10.4 0.4 C2 B:GHP4 3.4 5.5 1.0 O5 B:BGC8 3.5 7.4 0.6 C6 B:BGC8 3.6 9.4 0.6 C6 B:BGC8 3.6 8.3 0.4 O B:HOH2014 3.8 34.2 1.0 C4 B:GHP4 3.8 6.4 1.0 C5 B:BGC8 3.9 8.2 0.6 CG B:OMY6 4.0 5.0 1.0 CE2 B:OMY6 4.0 5.9 1.0 O2 B:LAC23 4.0 23.7 1.0 C5 B:BGC8 4.0 7.6 0.4 O6 B:BGC8 4.0 13.2 0.6 C2 B:LAC23 4.1 17.0 1.0 O4 B:GHP4 4.1 4.9 0.4 O B:HOH2012 4.2 30.6 1.0 O B:HOH2006 4.2 21.8 1.0 O B:GHP4 4.2 5.6 1.0 C1 B:GHP4 4.2 4.3 1.0 C1 B:BGC8 4.3 5.8 0.4 C1 B:BGC8 4.4 5.8 0.6 C3 B:LAC23 4.4 22.9 1.0 CD2 B:OMY6 4.5 4.9 1.0 C5 B:GHP4 4.5 5.0 1.0 O4 B:GHP4 4.5 5.3 0.6 C B:GHP4 4.6 4.3 1.0 C6 B:GHP4 4.7 4.7 1.0

Chlorine binding site 5 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl21 b:5.4 occ:1.00 N A:3FG7 3.2 4.2 1.0 O A:HOH2018 3.2 11.2 1.0 CA A:OMY6 3.7 3.8 1.0 C2 A:GHP5 3.7 3.6 1.0 CD1 A:OMY6 3.8 4.0 1.0 CB A:3FG7 3.8 4.3 1.0 C A:OMY6 3.9 4.2 1.0 CB A:OMY6 3.9 4.2 1.0 CG1 A:3FG7 3.9 4.0 1.0 CA A:3FG7 4.1 4.9 1.0 CG2 A:3FG7 4.2 4.7 1.0 C3 A:GHP5 4.3 4.1 1.0 CD1 A:3FG7 4.3 4.2 1.0 CG A:OMY6 4.4 3.9 1.0 CD2 A:3FG7 4.6 4.3 1.0 C1 A:GHP5 4.6 3.5 1.0 CA A:GHP5 4.6 3.2 1.0 CZ A:3FG7 4.7 4.1 1.0 CE1 A:OMY6 4.8 4.4 1.0 N A:OMY6 4.9 3.8 1.0 O A:3FG7 4.9 7.3 1.0 CL A:OMY6 4.9 5.6 1.0

Chlorine binding site 6 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl20 b:9.5 occ:1.00 O4 B:RER9 3.1 6.4 1.0 N3 A:RER9 3.6 11.4 1.0 C3A A:RER9 3.6 8.4 1.0 C4 B:RER9 3.8 4.8 1.0 C5A B:RER9 4.0 7.0 1.0 C3 A:RER9 4.1 8.9 1.0 O A:HOH2011 4.4 25.2 1.0 C2 A:RER9 4.5 10.4 1.0 C5 B:RER9 4.5 6.0 1.0

Chlorine binding site 7 out of 7 in the Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Complex of Vancomycin with 2-Acetoxy-D-Propanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl10 b:12.7 occ:1.00 O B:HOH2006 3.0 21.8 1.0 N B:3FG7 3.2 5.3 1.0 CA B:OMY6 3.6 4.3 1.0 C2 B:GHP5 3.7 4.9 1.0 CD1 B:OMY6 3.8 5.7 1.0 CB B:OMY6 3.8 4.8 1.0 C B:OMY6 3.9 4.7 1.0 CB B:3FG7 4.1 6.7 1.0 O B:HOH2014 4.2 34.2 1.0 CA B:3FG7 4.2 7.0 1.0 CG1 B:3FG7 4.3 6.7 1.0 CG B:OMY6 4.3 5.0 1.0 CA B:GHP5 4.5 4.3 1.0 C3 B:GHP5 4.5 5.4 1.0 CG2 B:3FG7 4.5 8.3 1.0 C1 B:GHP5 4.6 4.4 1.0 N B:OMY6 4.7 3.9 1.0 O B:3FG7 4.7 16.3 1.0 CE1 B:OMY6 4.8 6.7 1.0 CD1 B:3FG7 4.8 7.5 1.0

P.J.Loll, J.Kaplan, B.S.Selinsky, P.H.Axelsen. Vancomycin Binding to Low-Affinity Ligands: Delineating A Minimum Set of Interactions Necessary For High-Affinity Binding. J.Med.Chem. V. 42 4714 1999.
ISSN: ISSN 0022-2623
PubMed: 10579833
DOI: 10.1021/JM990361T