Chlorine in PDB 1ghg: Crystal Structure of Vancomycin Aglycon

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

Resolution Low / High (Å)	8.00 / 0.98
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	29.480, 29.480, 74.270, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 15

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

Chlorine binding site 1 out of 8 in the Crystal Structure of Vancomycin Aglycon


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 Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:12.2 occ:1.00 CL A:OMZ2 0.0 12.2 1.0 CE1 A:OMZ2 1.7 9.9 1.0 CZ A:OMZ2 2.7 9.8 1.0 CD1 A:OMZ2 2.7 10.1 1.0 OH A:OMZ2 2.9 9.6 1.0 C5 A:GHP4 3.6 8.7 1.0 O B:HOH2012 3.6 12.8 1.0 O A:HOH2006 3.6 27.4 1.0 C6 A:GHP4 3.7 7.7 1.0 O A:HOH2004 3.7 20.9 1.0 CD2 B:OMY6 3.8 8.7 1.0 CE2 A:OMZ2 4.0 9.8 1.0 CG A:OMZ2 4.0 9.7 1.0 O A:HOH2009 4.1 10.3 1.0 ODE B:OMY6 4.2 8.4 1.0 O B:HOH2006 4.2 25.8 1.0 CE2 B:OMY6 4.3 9.3 1.0 CD2 A:OMZ2 4.4 8.9 1.0 CG B:OMY6 4.6 8.2 1.0 C4 A:GHP4 4.7 8.7 1.0 O A:ASN3 4.8 8.6 1.0 C1 A:GHP4 4.9 7.4 1.0 O A:HOH2012 5.0 25.4 1.0 CB B:OMY6 5.0 8.0 1.0 O A:OMZ2 5.0 10.0 1.0

Chlorine binding site 2 out of 8 in the Crystal Structure of Vancomycin Aglycon


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 Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:8.6 occ:1.00 CL A:OMY6 0.0 8.6 1.0 CE1 A:OMY6 1.7 8.5 1.0 CD1 A:OMY6 2.7 8.4 1.0 CZ A:OMY6 2.7 8.0 1.0 OCZ A:OMY6 3.0 8.7 1.0 C3 A:GHP4 3.1 7.9 1.0 C2 A:GHP4 3.3 8.4 1.0 CH3 A:ACY11 3.5 9.0 1.0 C4 A:GHP4 3.8 8.7 1.0 CE2 A:OMY6 3.9 8.8 1.0 CG A:OMY6 3.9 8.7 1.0 C1 A:GHP4 4.2 7.4 1.0 O4 A:GHP4 4.3 9.5 1.0 CD2 A:OMY6 4.5 8.4 1.0 C5 A:GHP4 4.5 8.7 1.0 O A:GHP4 4.6 8.4 1.0 C6 A:GHP4 4.7 7.7 1.0 C A:GHP4 4.7 7.6 1.0 C A:ACY11 5.0 8.2 1.0

Chlorine binding site 3 out of 8 in the Crystal Structure of Vancomycin Aglycon


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 Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:10.5 occ:1.00 CL B:OMZ2 0.0 10.5 1.0 CE1 B:OMZ2 1.7 9.8 1.0 CD1 B:OMZ2 2.7 9.8 1.0 CZ B:OMZ2 2.7 9.0 1.0 OH B:OMZ2 3.0 8.7 1.0 C5 B:GHP4 3.4 7.9 1.0 C6 B:GHP4 3.5 8.3 1.0 CD2 A:OMY6 3.5 8.4 1.0 CE2 A:OMY6 3.8 8.8 1.0 CG B:OMZ2 4.0 8.9 1.0 CE2 B:OMZ2 4.0 9.2 1.0 C4 B:GHP4 4.4 8.3 1.0 CD2 B:OMZ2 4.5 9.5 1.0 C1 B:GHP4 4.5 8.2 1.0 ODE A:OMY6 4.5 9.3 1.0 CG A:OMY6 4.6 8.7 1.0 O B:ASN3 4.7 10.5 1.0 CZ A:OMY6 4.9 8.0 1.0 O4 B:GHP4 4.9 9.7 1.0 C B:ASN3 4.9 8.4 1.0

Chlorine binding site 4 out of 8 in the Crystal Structure of Vancomycin Aglycon


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 Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:11.7 occ:1.00 CL B:OMY6 0.0 11.7 1.0 CE1 B:OMY6 1.7 9.1 1.0 CD1 B:OMY6 2.7 8.6 1.0 CZ B:OMY6 2.7 8.3 1.0 OCZ B:OMY6 3.0 9.2 1.0 C3 B:GHP4 3.2 8.0 1.0 C2 B:GHP4 3.6 8.4 1.0 C4 B:GHP4 3.8 8.3 1.0 CE2 B:OMY6 4.0 9.3 1.0 CG B:OMY6 4.0 8.2 1.0 O4 B:GHP4 4.3 9.7 1.0 C1 B:GHP4 4.5 8.2 1.0 CD2 B:OMY6 4.5 8.7 1.0 CH3 B:ACY11 4.6 22.3 1.0 C5 B:GHP4 4.6 7.9 1.0 O B:GHP4 4.8 8.7 1.0 C6 B:GHP4 4.9 8.3 1.0 O B:HOH2009 4.9 26.7 1.0 O B:HOH2013 5.0 13.9 1.0

Chlorine binding site 5 out of 8 in the Crystal Structure of Vancomycin Aglycon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Vancomycin Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2 b:9.6 occ:1.00 CL C:OMZ2 0.0 9.6 1.0 CE1 C:OMZ2 1.7 8.7 1.0 CD1 C:OMZ2 2.7 8.7 1.0 CZ C:OMZ2 2.7 8.2 1.0 OH C:OMZ2 3.0 8.2 1.0 CE2 D:OMY6 3.5 8.0 1.0 C5 C:GHP4 3.5 7.4 1.0 CD2 D:OMY6 3.5 8.2 1.0 C6 C:GHP4 3.6 7.3 1.0 CE2 C:OMZ2 3.9 8.7 1.0 CG C:OMZ2 4.0 8.2 1.0 O C:HOH2005 4.0 11.3 1.0 CZ D:OMY6 4.4 8.3 1.0 CD2 C:OMZ2 4.4 8.3 1.0 C4 C:GHP4 4.5 8.2 1.0 CG D:OMY6 4.5 7.7 1.0 C1 C:GHP4 4.7 7.8 1.0 O4 C:GHP4 4.9 10.2 1.0 OCZ D:OMY6 4.9 8.7 1.0 O C:OMZ2 5.0 9.1 1.0

Chlorine binding site 6 out of 8 in the Crystal Structure of Vancomycin Aglycon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Vancomycin Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl6 b:10.9 occ:1.00 CL C:OMY6 0.0 10.9 1.0 CE1 C:OMY6 1.8 9.7 1.0 CD1 C:OMY6 2.7 9.9 1.0 CZ C:OMY6 2.7 9.0 1.0 OCZ C:OMY6 3.0 9.2 1.0 C3 C:GHP4 3.2 7.8 1.0 C2 C:GHP4 3.6 7.9 1.0 C1 C:DMS12 3.8 23.4 1.0 C4 C:GHP4 3.8 8.2 1.0 CE2 C:OMY6 4.0 9.9 1.0 CG C:OMY6 4.0 9.8 1.0 O4 C:GHP4 4.2 10.2 1.0 C1 C:GHP4 4.5 7.8 1.0 CH3 C:ACY11 4.5 9.9 1.0 CD2 C:OMY6 4.5 9.7 1.0 O C:GHP4 4.5 8.6 1.0 O C:DMS12 4.6 12.2 1.0 C5 C:GHP4 4.6 7.4 1.0 S C:DMS12 4.9 15.8 1.0 C6 C:GHP4 4.9 7.3 1.0 C C:GHP4 5.0 8.0 1.0

Chlorine binding site 7 out of 8 in the Crystal Structure of Vancomycin Aglycon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Vancomycin Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl2 b:17.9 occ:1.00 CL D:OMZ2 0.0 17.9 1.0 CE1 D:OMZ2 1.7 13.6 1.0 CD1 D:OMZ2 2.7 14.7 1.0 CZ D:OMZ2 2.7 12.5 1.0 OH D:OMZ2 3.0 12.7 1.0 C5 D:GHP4 3.5 10.0 1.0 C6 D:GHP4 3.5 10.0 1.0 CE2 C:OMY6 3.9 9.9 1.0 CD2 C:OMY6 3.9 9.7 1.0 CE2 D:OMZ2 4.0 12.5 1.0 CG D:OMZ2 4.0 14.4 1.0 O D:HOH2004 4.5 17.9 1.0 O D:ASN3 4.5 12.7 1.0 C4 D:GHP4 4.5 9.3 1.0 CD2 D:OMZ2 4.5 14.1 1.0 C1 D:GHP4 4.6 8.3 1.0 CZ C:OMY6 4.8 9.0 1.0 C D:ASN3 4.8 11.3 1.0 O D:OMZ2 4.9 14.0 1.0 CG C:OMY6 4.9 9.8 1.0

Chlorine binding site 8 out of 8 in the Crystal Structure of Vancomycin Aglycon


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Vancomycin Aglycon within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl6 b:9.2 occ:1.00 CL D:OMY6 0.0 9.2 1.0 CE1 D:OMY6 1.7 8.0 1.0 CD1 D:OMY6 2.7 7.5 1.0 CZ D:OMY6 2.7 8.3 1.0 OCZ D:OMY6 3.0 8.7 1.0 C3 D:GHP4 3.0 8.2 1.0 C2 D:GHP4 3.4 8.0 1.0 O D:HOH2007 3.5 17.9 1.0 C4 D:GHP4 3.6 9.3 1.0 C2 D:DMS12 3.8 12.9 1.0 CH3 D:ACY11 3.9 12.2 1.0 CE2 D:OMY6 4.0 8.0 1.0 CG D:OMY6 4.0 7.7 1.0 O4 D:GHP4 4.0 11.2 1.0 C1 D:GHP4 4.1 8.3 1.0 O D:GHP4 4.2 9.0 1.0 C5 D:GHP4 4.3 10.0 1.0 C6 D:GHP4 4.5 10.0 1.0 CD2 D:OMY6 4.5 8.2 1.0 S D:DMS12 4.6 10.6 1.0 C D:GHP4 4.7 8.3 1.0 O D:DMS12 4.7 9.5 1.0

J.Kaplan, B.D.Korty, P.H.Axelsen, P.J.Loll. The Role of Sugar Residues in Molecular Recognition By Vancomycin J.Med.Chem. V. 44 1837 2001.
ISSN: ISSN 0022-2623
PubMed: 11356118
DOI: 10.1021/JM0005306