Chlorine in PDB 1aa5: Vancomycin

The structure of Vancomycin, PDB code: 1aa5 was solved by P.J.Loll, A.E.Bevivino, B.D.Korty, P.H.Axelsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	4.00 / 0.89
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	28.450, 28.450, 65.840, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / n/a

The binding sites of Chlorine atom in the Vancomycin (pdb code 1aa5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Vancomycin, PDB code: 1aa5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:7.2 occ:1.00 CL A:OMZ2 0.0 7.2 1.0 CE1 A:OMZ2 1.7 4.5 1.0 CD1 A:OMZ2 2.7 4.0 1.0 CZ A:OMZ2 2.7 4.4 1.0 HD2 B:OMY6 2.8 6.7 1.0 HD1 A:OMZ2 2.8 6.0 1.0 OH A:OMZ2 3.0 5.0 1.0 HDE B:OMY6 3.1 6.9 1.0 H6 A:GHP4 3.3 5.5 1.0 H6C1 A:BGC8 3.4 17.2 1.0 C5 A:GHP4 3.4 3.9 1.0 CD2 B:OMY6 3.5 4.5 1.0 C6 A:GHP4 3.6 3.6 1.0 O B:HOH2009 3.7 14.5 1.0 HE2 B:OMY6 3.7 8.0 1.0 H6 A:BGC8 3.7 20.7 1.0 O A:HOH2025 3.8 18.4 0.5 ODE B:OMY6 3.9 4.6 1.0 CE2 B:OMY6 4.0 5.3 1.0 CE2 A:OMZ2 4.0 4.3 1.0 CG A:OMZ2 4.0 3.7 1.0 O5 A:BGC8 4.1 6.9 1.0 C6 A:BGC8 4.2 11.5 1.0 O6 A:BGC8 4.2 13.8 1.0 C4 A:GHP4 4.4 3.7 1.0 CG B:OMY6 4.5 4.6 1.0 CD2 A:OMZ2 4.5 3.9 1.0 O A:ASN3 4.6 3.3 1.0 C1 A:GHP4 4.7 3.1 1.0 HE2 A:OMZ2 4.7 6.5 1.0 CB B:OMY6 4.8 4.5 1.0 C5 A:BGC8 4.8 9.2 1.0 O4 A:GHP4 4.9 4.6 1.0 H6C2 A:BGC8 4.9 17.2 1.0 HN1 B:OMY6 4.9 5.4 1.0

Chlorine binding site 2 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:5.2 occ:1.00 CL A:OMY6 0.0 5.2 1.0 CE1 A:OMY6 1.8 4.1 1.0 CD1 A:OMY6 2.7 3.7 1.0 CZ A:OMY6 2.7 3.7 1.0 HD1 A:OMY6 2.8 5.5 1.0 OCZ A:OMY6 3.0 4.4 1.0 H3A1 A:RER9 3.1 11.9 1.0 C3 A:GHP4 3.2 3.9 1.0 H5 A:RER9 3.3 14.2 1.0 H3A2 A:RER9 3.4 11.9 1.0 C2 A:GHP4 3.4 3.5 1.0 HC2 A:GHP4 3.5 5.3 1.0 H4 A:RER9 3.6 15.0 1.0 C3A A:RER9 3.7 7.9 1.0 H5A2 A:RER9 3.7 18.7 1.0 C4 A:GHP4 3.9 3.7 1.0 C5 A:RER9 4.0 9.4 1.0 CG A:OMY6 4.0 3.4 1.0 CE2 A:OMY6 4.0 3.7 1.0 C4 A:RER9 4.1 10.0 1.0 C1 A:GHP4 4.2 3.1 1.0 C5A A:RER9 4.3 12.5 1.0 O4 A:GHP4 4.3 4.6 1.0 H3A3 A:RER9 4.4 11.9 1.0 HA A:GHP5 4.4 4.8 1.0 CD2 A:OMY6 4.5 3.7 1.0 C3 A:RER9 4.6 8.1 1.0 C5 A:GHP4 4.6 3.9 1.0 O A:GHP4 4.6 3.2 1.0 H5A1 A:RER9 4.6 18.7 1.0 C6 A:GHP4 4.7 3.6 1.0 HE2 A:OMY6 4.8 5.5 1.0 C A:GHP4 4.8 3.0 1.0 O4 A:RER9 4.9 6.4 0.2 HA A:OMY6 4.9 5.7 1.0 CL A:CL21 4.9 4.9 1.0

Chlorine binding site 3 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:5.1 occ:1.00 CL B:OMZ2 0.0 5.1 1.0 CE1 B:OMZ2 1.8 4.1 1.0 CD1 B:OMZ2 2.7 4.6 1.0 CZ B:OMZ2 2.7 4.6 1.0 HD1 B:OMZ2 2.8 6.9 1.0 OH B:OMZ2 3.0 5.0 1.0 H6 B:GHP4 3.2 6.2 1.0 H4 B:RER9 3.2 6.7 1.0 H5A2 B:RER9 3.2 10.5 1.0 HD2 A:OMY6 3.3 5.6 1.0 C5 B:GHP4 3.4 4.4 1.0 C6 B:GHP4 3.5 4.1 1.0 H5 B:RER9 3.5 8.4 1.0 H3A1 B:RER9 3.6 6.1 1.0 HE2 A:OMY6 3.9 5.5 1.0 CD2 A:OMY6 3.9 3.7 1.0 C4 B:RER9 4.0 4.5 1.0 C5 B:RER9 4.0 5.6 1.0 C5A B:RER9 4.0 7.0 1.0 CE2 B:OMZ2 4.0 5.4 1.0 CG B:OMZ2 4.0 4.9 1.0 O B:HOH2001 4.0 9.0 1.0 H3A2 B:RER9 4.0 6.1 1.0 C3A B:RER9 4.2 4.1 1.0 CE2 A:OMY6 4.2 3.7 1.0 H5A1 B:RER9 4.4 10.5 1.0 C4 B:GHP4 4.5 5.9 1.0 CD2 B:OMZ2 4.5 6.0 1.0 C1 B:GHP4 4.5 3.7 1.0 O B:ASN3 4.7 5.2 1.0 H5A3 B:RER9 4.7 10.5 1.0 C3 B:RER9 4.7 4.0 1.0 HE2 B:OMZ2 4.7 8.1 1.0 ODE A:OMY6 4.8 4.5 1.0 H32N B:RER9 4.9 5.8 1.0 C B:ASN3 4.9 3.8 1.0 O B:OMZ2 4.9 5.8 1.0 CG A:OMY6 5.0 3.4 1.0

Chlorine binding site 4 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:8.1 occ:1.00 CL B:OMY6 0.0 8.1 1.0 CE1 B:OMY6 1.8 5.7 1.0 CD1 B:OMY6 2.7 5.2 1.0 CZ B:OMY6 2.7 5.3 1.0 HD1 B:OMY6 2.8 7.8 1.0 H6C2 B:BGC8 2.8 12.5 0.3 OCZ B:OMY6 3.0 6.8 1.0 H6C2 B:BGC8 3.1 12.4 0.7 O6 B:BGC8 3.1 9.6 0.7 C3 B:GHP4 3.1 5.6 1.0 O5 B:BGC8 3.2 6.2 0.7 H6 B:BGC8 3.3 17.4 0.3 C2 B:GHP4 3.5 4.5 1.0 O B:HOH2013 3.5 23.4 1.0 C6 B:BGC8 3.5 8.2 0.7 O B:HOH2019 3.5 6.4 0.3 O5 B:BGC8 3.6 5.9 0.3 C6 B:BGC8 3.6 8.3 0.3 HC2 B:GHP4 3.6 6.8 1.0 H3 A:ACY11 3.6 16.1 1.0 O6 B:BGC8 3.7 11.6 0.3 H6 B:BGC8 3.8 14.3 0.7 C4 B:GHP4 3.8 5.9 1.0 O B:HOH2006 3.9 16.5 1.0 CG B:OMY6 4.0 4.6 1.0 H5 B:BGC8 4.0 10.5 0.3 C5 B:BGC8 4.0 7.0 0.3 CE2 B:OMY6 4.0 5.3 1.0 O B:HOH2020 4.0 13.1 0.3 C5 B:BGC8 4.0 7.2 0.7 CH3 A:ACY11 4.2 10.8 1.0 O4 B:GHP4 4.2 4.7 0.7 H1 A:ACY11 4.2 16.1 1.0 H2 A:ACY11 4.3 16.1 1.0 O B:GHP4 4.3 4.8 1.0 C1 B:BGC8 4.3 5.3 0.7 C1 B:GHP4 4.3 3.7 1.0 H6C1 B:BGC8 4.4 12.5 0.3 H6C1 B:BGC8 4.4 12.4 0.7 HA B:GHP5 4.4 5.7 1.0 C1 B:BGC8 4.4 4.6 0.3 H1 B:BGC8 4.4 7.0 0.3 CD2 B:OMY6 4.5 4.5 1.0 O B:HOH2014 4.5 38.3 1.0 H5 B:BGC8 4.6 10.7 0.7 O4 B:GHP4 4.6 4.5 0.3 C5 B:GHP4 4.6 4.4 1.0 H1 B:BGC8 4.7 8.0 0.7 C B:GHP4 4.7 3.5 1.0 HE2 B:OMY6 4.7 8.0 1.0 C6 B:GHP4 4.8 4.1 1.0 H5 A:BGC8 5.0 13.8 1.0

Chlorine binding site 5 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl21 b:4.9 occ:1.00 HN1 A:3FG7 2.4 5.7 1.0 HC2 A:GHP5 2.9 4.6 1.0 HD1 A:OMY6 2.9 5.5 1.0 HA A:OMY6 3.0 5.7 1.0 N A:3FG7 3.2 3.8 1.0 O A:HOH2021 3.3 8.1 1.0 HB A:OMY6 3.4 5.7 1.0 CA A:OMY6 3.7 3.8 1.0 C2 A:GHP5 3.7 3.1 1.0 CD1 A:OMY6 3.8 3.7 1.0 HA A:GHP5 3.9 4.8 1.0 CB A:3FG7 3.9 4.1 1.0 CB A:OMY6 3.9 3.8 1.0 C A:OMY6 3.9 3.5 1.0 CG1 A:3FG7 4.0 3.8 1.0 CA A:3FG7 4.1 4.6 1.0 CG2 A:3FG7 4.3 4.5 1.0 C3 A:GHP5 4.3 3.6 1.0 CG A:OMY6 4.4 3.4 1.0 CD1 A:3FG7 4.4 3.6 1.0 HG2 A:3FG7 4.6 6.8 1.0 CA A:GHP5 4.7 3.2 1.0 C1 A:GHP5 4.7 3.3 1.0 CD2 A:3FG7 4.7 4.3 1.0 CZ A:3FG7 4.8 3.7 1.0 CE1 A:OMY6 4.8 4.1 1.0 HA A:3FG7 4.8 6.9 1.0 OXT A:3FG7 4.8 6.4 1.0 N A:OMY6 4.9 3.3 1.0 CL A:OMY6 4.9 5.2 1.0

Chlorine binding site 6 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl22 b:15.4 occ:1.00 HD2 A:OMZ2 2.6 5.8 1.0 HA A:MLU1 2.6 6.3 1.0 H A:OMZ2 2.8 5.2 1.0 O A:HOH2003 2.9 16.2 0.5 O A:HOH2005 2.9 17.6 1.0 HCN2 A:MLU1 3.0 11.0 1.0 N A:OMZ2 3.4 3.4 1.0 CA A:MLU1 3.5 4.2 1.0 CD2 A:OMZ2 3.5 3.9 1.0 HD21 A:MLU1 3.7 11.8 0.7 CN A:MLU1 3.8 7.3 1.0 OC A:OMZ2 3.8 4.3 1.0 C A:MLU1 3.9 3.8 1.0 HCN3 A:MLU1 4.0 11.0 1.0 N A:MLU1 4.1 5.0 1.0 HE2 A:OMZ2 4.1 6.5 1.0 HC A:OMZ2 4.2 6.4 1.0 H A:MLU1 4.2 7.5 1.0 CE2 A:OMZ2 4.3 4.3 1.0 CG A:OMZ2 4.4 3.7 1.0 CB A:OMZ2 4.4 3.8 1.0 HD23 A:MLU1 4.5 11.8 0.7 CD2 A:MLU1 4.5 7.8 0.7 CA A:OMZ2 4.5 3.7 1.0 HCN1 A:MLU1 4.6 11.0 1.0 CB A:MLU1 4.6 4.3 1.0 HB3 A:MLU1 4.7 6.5 1.0 O A:HOH2006 4.9 14.4 0.4

Chlorine binding site 7 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl21 b:8.6 occ:1.00 H33N A:RER9 2.5 16.4 1.0 H3A3 A:RER9 2.8 11.9 1.0 O4 B:RER9 3.1 6.2 1.0 O A:HOH2013 3.2 27.6 1.0 HO4 B:RER9 3.2 9.2 1.0 H4 B:RER9 3.4 6.7 1.0 N3 A:RER9 3.4 11.0 1.0 H5A3 B:RER9 3.6 10.5 1.0 C3A A:RER9 3.6 7.9 1.0 H32N A:RER9 3.7 16.4 1.0 C4 B:RER9 3.8 4.5 1.0 H5A2 B:RER9 3.8 10.5 1.0 H21C A:RER9 3.8 14.5 1.0 H3A1 A:RER9 3.9 11.9 1.0 C5A B:RER9 4.1 7.0 1.0 C3 A:RER9 4.1 8.1 1.0 H31N A:RER9 4.1 16.4 1.0 O B:HOH2021 4.2 30.9 1.0 H3A2 A:RER9 4.4 11.9 1.0 C2 A:RER9 4.4 9.7 1.0 C5 B:RER9 4.5 5.6 1.0 H31N B:RER9 4.6 5.8 1.0 H32N B:RER9 4.6 5.8 1.0 H22C A:RER9 4.7 14.5 1.0 H5A1 B:RER9 4.9 10.5 1.0 N3 B:RER9 4.9 3.9 1.0

Chlorine binding site 8 out of 8 in the Vancomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Vancomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl22 b:10.9 occ:1.00 HN1 B:3FG7 2.4 7.2 1.0 HA B:OMY6 2.8 6.1 1.0 HC2 B:GHP5 2.9 7.0 1.0 HD1 B:OMY6 3.0 7.8 1.0 O B:HOH2006 3.0 16.5 1.0 N B:3FG7 3.2 4.8 1.0 HB B:OMY6 3.3 6.8 1.0 CA B:OMY6 3.6 4.1 1.0 HA B:GHP5 3.7 5.7 1.0 C2 B:GHP5 3.7 4.7 1.0 CD1 B:OMY6 3.8 5.2 1.0 CB B:OMY6 3.9 4.5 1.0 C B:OMY6 3.9 3.9 1.0 CB B:3FG7 4.1 6.3 1.0 CA B:3FG7 4.2 6.4 1.0 CG1 B:3FG7 4.3 6.1 1.0 CG B:OMY6 4.3 4.6 1.0 O B:HOH2013 4.5 23.4 1.0 CG2 B:3FG7 4.5 7.8 1.0 CA B:GHP5 4.5 3.8 1.0 C3 B:GHP5 4.5 5.2 1.0 C1 B:GHP5 4.6 4.3 1.0 HG2 B:3FG7 4.7 11.8 1.0 OXT B:3FG7 4.8 13.9 1.0 N B:OMY6 4.8 3.6 1.0 CD1 B:3FG7 4.8 7.3 1.0 CE1 B:OMY6 4.8 5.7 1.0 HA B:3FG7 5.0 9.6 1.0

P.J.Loll, A.E.Bevivino, B.D.Korty, P.H.Axelsen. Simultaneous Recognition of A Carboxylate-Containing Ligand and An Intramolecular Surrogate Ligand in the Crystal Structure of An Asymmetric Vancomycin Dimer. J.Am.Chem.Soc. V. 119 1516 1997.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA963566P