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Chlorine in PDB 1qd8: Complex of Vancomycin with N-Acetyl Glycine

Protein crystallography data

The structure of Complex of Vancomycin with N-Acetyl Glycine, PDB code: 1qd8 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 (°) 28.710, 28.710, 66.770, 90.00, 90.00, 90.00
R / Rfree (%) 11 / 13.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Complex of Vancomycin with N-Acetyl Glycine (pdb code 1qd8). 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 N-Acetyl Glycine, PDB code: 1qd8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 1qd8

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Chlorine binding site 1 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2

b:8.4
occ:1.00
 CL A:OMZ2 0.0 8.4 1.0
CE1 A:OMZ2 1.7 5.2 1.0
CZ A:OMZ2 2.7 4.9 1.0
CD1 A:OMZ2 2.7 4.8 1.0
OH A:OMZ2 3.0 5.7 1.0
C5 A:GHP4 3.4 4.6 1.0
CD2 B:OMY6 3.5 5.3 1.0
C6 A:GHP4 3.6 4.2 1.0
O A:HOH148 3.7 19.4 1.0
ODE B:OMY6 4.0 5.1 1.0
CE2 A:OMZ2 4.0 5.0 1.0
CG A:OMZ2 4.0 4.2 1.0
CE2 B:OMY6 4.0 5.8 1.0
O5 A:BGC8 4.1 7.5 1.0
C6 A:BGC8 4.2 11.3 1.0
O6 A:BGC8 4.3 14.0 1.0
C4 A:GHP4 4.4 4.5 1.0
CG B:OMY6 4.5 5.0 1.0
CD2 A:OMZ2 4.5 4.5 1.0
O A:ASN3 4.7 3.9 1.0
O A:HOH149 4.7 31.0 1.0
C1 A:GHP4 4.7 3.9 1.0
CL A:CL12 4.8 9.1 1.0
C5 A:BGC8 4.8 10.0 1.0
CB B:OMY6 4.9 4.8 1.0
O4 A:GHP4 5.0 5.3 1.0

Chlorine binding site 2 out of 7 in 1qd8

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Chlorine binding site 2 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl6

b:5.9
occ:1.00
 CL A:OMY6 0.0 5.9 1.0
CE1 A:OMY6 1.8 4.7 1.0
CD1 A:OMY6 2.7 4.4 1.0
CZ A:OMY6 2.8 4.3 1.0
OCZ A:OMY6 3.1 5.1 1.0
C3 A:GHP4 3.2 4.3 1.0
C2 A:GHP4 3.5 4.0 1.0
C3A A:RER9 3.7 8.4 1.0
C4 A:GHP4 3.9 4.5 1.0
C5 A:RER9 4.0 9.9 1.0
CG A:OMY6 4.0 4.0 1.0
CE2 A:OMY6 4.1 4.5 1.0
C4 A:RER9 4.1 10.3 1.0
C5A A:RER9 4.2 12.7 1.0
C1 A:GHP4 4.3 3.9 1.0
O4 A:GHP4 4.4 5.3 1.0
C3 A:RER9 4.6 8.6 1.0
CD2 A:OMY6 4.6 4.0 1.0
C5 A:GHP4 4.6 4.6 1.0
O A:GHP4 4.6 3.9 1.0
C6 A:GHP4 4.8 4.2 1.0
C A:GHP4 4.9 3.6 1.0
CL A:CL13 5.0 5.5 1.0

Chlorine binding site 3 out of 7 in 1qd8

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Chlorine binding site 3 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:5.9
occ:1.00
 CL B:OMZ2 0.0 5.9 1.0
CE1 B:OMZ2 1.8 4.8 1.0
CD1 B:OMZ2 2.7 4.9 1.0
CZ B:OMZ2 2.7 4.7 1.0
OH B:OMZ2 3.0 5.4 1.0
C5 B:GHP4 3.5 4.8 1.0
C6 B:GHP4 3.5 4.7 1.0
O A:HOH138 3.7 5.5 0.4
CD2 A:OMY6 3.9 4.0 1.0
O A:HOH147 4.0 11.4 1.0
C5 B:RER9 4.0 6.0 1.0
C5A B:RER9 4.0 7.2 1.0
C4 B:RER9 4.0 5.0 1.0
CE2 B:OMZ2 4.0 6.0 1.0
CG B:OMZ2 4.0 5.6 1.0
CE2 A:OMY6 4.2 4.5 1.0
C3A B:RER9 4.3 4.9 1.0
O A:HOH138 4.4 6.1 0.6
C4 B:GHP4 4.5 6.0 1.0
CD2 B:OMZ2 4.5 6.2 1.0
C1 B:GHP4 4.6 4.2 1.0
O B:ASN3 4.7 5.9 1.0
C3 B:RER9 4.8 4.6 1.0
ODE A:OMY6 4.8 5.2 1.0
C B:ASN3 5.0 4.5 1.0
CG A:OMY6 5.0 4.0 1.0

Chlorine binding site 4 out of 7 in 1qd8

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Chlorine binding site 4 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:8.8
occ:1.00
 CL B:OMY6 0.0 8.8 1.0
CE1 B:OMY6 1.8 6.5 1.0
CD1 B:OMY6 2.7 5.5 1.0
CZ B:OMY6 2.8 6.0 1.0
OCZ B:OMY6 3.0 7.3 1.0
O6 B:BGC8 3.2 9.1 0.6
C3 B:GHP4 3.2 5.9 1.0
O5 B:BGC8 3.3 6.2 0.6
C2 B:GHP4 3.5 5.2 1.0
C6 B:BGC8 3.6 7.8 0.6
O5 B:BGC8 3.6 6.7 0.4
O A:HOH127 3.7 13.4 0.6
O6 B:BGC8 3.7 14.8 0.4
N1 B:AAC11 3.7 14.8 1.0
C4 B:GHP4 3.9 6.0 1.0
C3 B:AAC11 3.9 17.3 1.0
C6 B:BGC8 4.0 10.1 0.4
CG B:OMY6 4.0 5.0 1.0
C5 B:BGC8 4.0 7.7 0.4
CE2 B:OMY6 4.0 5.8 1.0
O A:HOH131 4.1 28.3 1.0
C4 B:AAC11 4.1 20.7 1.0
C5 B:BGC8 4.1 7.2 0.6
C2 B:AAC11 4.2 10.8 1.0
O4 B:GHP4 4.3 5.2 0.6
O B:GHP4 4.4 5.5 1.0
C1 B:GHP4 4.4 4.2 1.0
C1 B:BGC8 4.4 5.5 0.6
O3 B:AAC11 4.5 22.4 1.0
C1 B:BGC8 4.5 5.5 0.4
CD2 B:OMY6 4.6 5.3 1.0
C5 B:GHP4 4.7 4.8 1.0
O4 B:GHP4 4.7 5.3 0.4
C B:GHP4 4.8 4.3 1.0
C6 B:GHP4 4.9 4.7 1.0

Chlorine binding site 5 out of 7 in 1qd8

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Chlorine binding site 5 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl12

b:9.1
occ:1.00
 CD1 A:OMZ2 3.6 4.8 1.0
CB A:OMZ2 3.9 4.4 1.0
CG A:OMZ2 4.1 4.2 1.0
O A:OMZ2 4.4 4.5 1.0
OC A:OMZ2 4.5 4.9 1.0
CE1 A:OMZ2 4.5 5.2 1.0
CL A:OMZ2 4.8 8.4 1.0

Chlorine binding site 6 out of 7 in 1qd8

Go back to Chlorine Binding Sites List in 1qd8
Chlorine binding site 6 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl13

b:5.5
occ:1.00
 N A:3FG7 3.2 4.7 1.0
CA A:OMY6 3.7 4.2 1.0
C2 A:GHP5 3.8 3.9 1.0
CD1 A:OMY6 3.8 4.4 1.0
CB A:3FG7 3.9 4.6 1.0
CB A:OMY6 4.0 4.2 1.0
C A:OMY6 4.0 4.5 1.0
CG1 A:3FG7 4.0 4.3 1.0
CA A:3FG7 4.2 5.1 1.0
CG2 A:3FG7 4.3 5.0 1.0
C3 A:GHP5 4.4 4.3 1.0
CG A:OMY6 4.4 4.0 1.0
CD1 A:3FG7 4.4 4.3 1.0
CA A:GHP5 4.7 3.7 1.0
C1 A:GHP5 4.7 3.9 1.0
CD2 A:3FG7 4.7 4.6 1.0
CZ A:3FG7 4.8 4.6 1.0
CE1 A:OMY6 4.8 4.7 1.0
O A:3FG7 4.9 7.2 1.0
N A:OMY6 5.0 4.0 1.0
CL A:OMY6 5.0 5.9 1.0

Chlorine binding site 7 out of 7 in 1qd8

Go back to Chlorine Binding Sites List in 1qd8
Chlorine binding site 7 out of 7 in the Complex of Vancomycin with N-Acetyl Glycine


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 N-Acetyl Glycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl12

b:11.3
occ:1.00
 N B:3FG7 3.2 5.7 1.0
O A:HOH130 3.3 27.8 1.0
CA B:OMY6 3.6 4.4 1.0
C4 B:AAC11 3.6 20.7 1.0
CD1 B:OMY6 3.8 5.5 1.0
C2 B:GHP5 3.8 5.3 1.0
CB B:OMY6 3.9 4.8 1.0
C B:OMY6 3.9 4.5 1.0
CB B:3FG7 4.1 7.0 1.0
CA B:3FG7 4.2 6.9 1.0
CG1 B:3FG7 4.3 7.0 1.0
CG B:OMY6 4.4 5.0 1.0
CG2 B:3FG7 4.6 8.8 1.0
C3 B:GHP5 4.6 5.8 1.0
CA B:GHP5 4.6 4.3 1.0
C1 B:GHP5 4.7 4.6 1.0
O B:3FG7 4.8 13.2 1.0
N B:OMY6 4.9 4.1 1.0
CE1 B:OMY6 4.9 6.5 1.0
CD1 B:3FG7 4.9 8.5 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: Sat Dec 12 08:46:49 2020

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