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Chlorine in PDB 1c0r: Complex of Vancomycin with D-Lactic Acid

Protein crystallography data

The structure of Complex of Vancomycin with D-Lactic Acid, PDB code: 1c0r 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 (°) 28.440, 28.440, 66.040, 90.00, 90.00, 90.00
R / Rfree (%) 11.4 / 14.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Complex of Vancomycin with D-Lactic Acid (pdb code 1c0r). 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 D-Lactic Acid, PDB code: 1c0r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 1c0r

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Chlorine binding site 1 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2

b:10.8
occ:1.00
 CL A:OMZ2 0.0 10.8 1.0
CE1 A:OMZ2 1.7 5.9 1.0
CD1 A:OMZ2 2.7 5.7 1.0
CZ A:OMZ2 2.7 5.7 1.0
OH A:OMZ2 3.0 6.2 1.0
C5 A:GHP4 3.4 5.3 1.0
CD2 B:OMY6 3.4 5.9 1.0
C6 A:GHP4 3.6 4.6 1.0
O B:HOH2008 3.7 18.1 1.0
ODE B:OMY6 3.9 5.8 1.0
CE2 B:OMY6 3.9 7.0 1.0
CE2 A:OMZ2 4.0 5.8 1.0
CG A:OMZ2 4.0 4.8 1.0
O5 A:BGC8 4.1 8.2 1.0
C6 A:BGC8 4.2 12.2 1.0
O6 A:BGC8 4.2 15.1 1.0
C4 A:GHP4 4.4 5.5 1.0
CG B:OMY6 4.4 5.7 1.0
CD2 A:OMZ2 4.5 5.4 1.0
O A:ASN3 4.6 4.6 1.0
C1 A:GHP4 4.7 4.3 1.0
CB B:OMY6 4.8 5.5 1.0
C5 A:BGC8 4.8 10.4 1.0
O A:HOH2008 4.9 29.6 1.0
O4 A:GHP4 4.9 6.1 1.0

Chlorine binding site 2 out of 7 in 1c0r

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Chlorine binding site 2 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl6

b:7.5
occ:1.00
 CL A:OMY6 0.0 7.5 1.0
CE1 A:OMY6 1.7 5.3 1.0
CD1 A:OMY6 2.7 5.2 1.0
CZ A:OMY6 2.8 5.1 1.0
OCZ A:OMY6 3.1 5.9 1.0
C3 A:GHP4 3.2 5.0 1.0
C2 A:GHP4 3.5 4.4 1.0
C3A A:RER9 3.7 9.3 1.0
C4 A:GHP4 3.9 5.5 1.0
C5 A:RER9 4.0 10.9 1.0
CG A:OMY6 4.0 5.0 1.0
CE2 A:OMY6 4.0 5.1 1.0
C4 A:RER9 4.2 11.0 1.0
C1 A:GHP4 4.3 4.3 1.0
O4 A:GHP4 4.3 6.1 1.0
C5A A:RER9 4.4 13.4 1.0
CD2 A:OMY6 4.5 4.9 1.0
C3 A:RER9 4.5 9.6 1.0
O A:GHP4 4.6 4.5 1.0
C5 A:GHP4 4.6 5.3 1.0
C6 A:GHP4 4.8 4.6 1.0
C A:GHP4 4.8 3.9 1.0
CL A:CL21 4.9 6.5 1.0

Chlorine binding site 3 out of 7 in 1c0r

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Chlorine binding site 3 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:7.6
occ:1.00
 CL B:OMZ2 0.0 7.6 1.0
CE1 B:OMZ2 1.7 5.2 1.0
CD1 B:OMZ2 2.7 5.5 1.0
CZ B:OMZ2 2.7 5.5 1.0
OH B:OMZ2 3.0 6.1 1.0
C5 B:GHP4 3.4 5.7 1.0
C6 B:GHP4 3.5 5.4 1.0
CD2 A:OMY6 3.9 4.9 1.0
C5 B:RER9 3.9 6.9 1.0
C4 B:RER9 4.0 6.1 1.0
C5A B:RER9 4.0 7.8 1.0
CE2 B:OMZ2 4.0 6.6 1.0
CG B:OMZ2 4.0 6.4 1.0
O B:HOH2001 4.0 11.7 1.0
C3A B:RER9 4.2 5.3 1.0
CE2 A:OMY6 4.2 5.1 1.0
C4 B:GHP4 4.5 7.0 1.0
CD2 B:OMZ2 4.5 7.1 1.0
C1 B:GHP4 4.6 4.9 1.0
C3 B:RER9 4.7 5.2 1.0
O B:ASN3 4.7 6.5 1.0
ODE A:OMY6 4.8 5.8 1.0
C B:ASN3 5.0 5.2 1.0
O4 B:GHP4 5.0 5.7 0.3
CG A:OMY6 5.0 5.0 1.0
O B:OMZ2 5.0 6.8 1.0

Chlorine binding site 4 out of 7 in 1c0r

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Chlorine binding site 4 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:11.3
occ:1.00
 CL B:OMY6 0.0 11.3 1.0
CE1 B:OMY6 1.8 8.0 1.0
CD1 B:OMY6 2.7 6.5 1.0
CZ B:OMY6 2.8 6.9 1.0
OCZ B:OMY6 3.1 8.8 1.0
O6 B:BGC8 3.2 11.8 0.7
C3 B:GHP4 3.2 7.1 1.0
O5 B:BGC8 3.3 7.1 0.7
C6 B:BGC8 3.3 9.6 0.3
O5 B:BGC8 3.5 7.6 0.3
C3 B:LAC23 3.6 13.7 1.0
C2 B:GHP4 3.6 6.4 1.0
C6 B:BGC8 3.6 9.6 0.7
O6 B:BGC8 3.9 12.4 0.3
C5 B:BGC8 3.9 8.8 0.3
C4 B:GHP4 3.9 7.0 1.0
CG B:OMY6 4.0 5.7 1.0
CE2 B:OMY6 4.1 7.0 1.0
C5 B:BGC8 4.1 8.7 0.7
O B:HOH2017 4.1 33.8 1.0
O2 B:LAC23 4.3 14.6 1.0
O4 B:GHP4 4.3 6.3 0.7
O B:GHP4 4.4 6.1 1.0
C1 B:BGC8 4.4 6.8 0.7
C1 B:GHP4 4.4 4.9 1.0
C1 B:BGC8 4.5 6.4 0.3
C2 B:LAC23 4.5 12.7 1.0
CD2 B:OMY6 4.5 5.9 1.0
O B:HOH2006 4.6 27.2 0.8
O4 B:GHP4 4.7 5.7 0.3
C5 B:GHP4 4.7 5.7 1.0
C B:GHP4 4.8 4.8 1.0
C6 B:GHP4 4.9 5.4 1.0
CL B:CL22 4.9 13.9 1.0

Chlorine binding site 5 out of 7 in 1c0r

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Chlorine binding site 5 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl20

b:10.6
occ:1.00
 O4 B:RER9 3.1 7.3 1.0
N3 A:RER9 3.4 11.8 1.0
C3A A:RER9 3.7 9.3 1.0
C4 B:RER9 3.8 6.1 1.0
C5A B:RER9 4.1 7.8 1.0
C3 A:RER9 4.1 9.6 1.0
C2 A:RER9 4.4 10.1 1.0
C5 B:RER9 4.6 6.9 1.0
N3 B:RER9 5.0 5.5 1.0

Chlorine binding site 6 out of 7 in 1c0r

Go back to Chlorine Binding Sites List in 1c0r
Chlorine binding site 6 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl21

b:6.5
occ:1.00
 N A:3FG7 3.2 4.9 1.0
O A:HOH2019 3.2 11.1 1.0
CA A:OMY6 3.7 4.6 1.0
C2 A:GHP5 3.7 4.2 1.0
CD1 A:OMY6 3.8 5.2 1.0
CB A:3FG7 3.9 5.2 1.0
C A:OMY6 3.9 4.6 1.0
CB A:OMY6 3.9 5.0 1.0
CG1 A:3FG7 4.0 4.5 1.0
CA A:3FG7 4.1 5.5 1.0
CG2 A:3FG7 4.3 5.4 1.0
C3 A:GHP5 4.3 5.0 1.0
CG A:OMY6 4.4 5.0 1.0
CD1 A:3FG7 4.4 4.8 1.0
C1 A:GHP5 4.7 4.3 1.0
CA A:GHP5 4.7 4.1 1.0
CD2 A:3FG7 4.7 5.0 1.0
CZ A:3FG7 4.8 4.7 1.0
CE1 A:OMY6 4.8 5.3 1.0
O A:3FG7 4.9 8.0 1.0
N A:OMY6 4.9 4.3 1.0
CL A:OMY6 4.9 7.5 1.0

Chlorine binding site 7 out of 7 in 1c0r

Go back to Chlorine Binding Sites List in 1c0r
Chlorine binding site 7 out of 7 in the Complex of Vancomycin with D-Lactic 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 D-Lactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl22

b:13.9
occ:1.00
 O B:HOH2006 3.0 27.2 0.8
N B:3FG7 3.2 6.0 1.0
O B:HOH2004 3.2 61.2 1.0
CA B:OMY6 3.5 4.8 1.0
C2 B:GHP5 3.7 5.8 1.0
CD1 B:OMY6 3.8 6.5 1.0
CB B:OMY6 3.8 5.5 1.0
C B:OMY6 3.9 5.1 1.0
CB B:3FG7 4.1 7.3 1.0
CA B:3FG7 4.2 7.3 1.0
CG1 B:3FG7 4.3 7.4 1.0
CG B:OMY6 4.3 5.7 1.0
CA B:GHP5 4.5 4.7 1.0
C3 B:GHP5 4.5 6.2 1.0
CG2 B:3FG7 4.6 9.2 1.0
C1 B:GHP5 4.6 5.0 1.0
O B:3FG7 4.7 14.3 1.0
N B:OMY6 4.7 4.7 1.0
CE1 B:OMY6 4.8 8.0 1.0
CD1 B:3FG7 4.9 8.5 1.0
CL B:OMY6 4.9 11.3 1.0

Reference:

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
Page generated: Fri Jul 19 21:07:16 2024

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