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Chlorine in PDB 1fvm: Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala

Protein crystallography data

The structure of Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala, PDB code: 1fvm was solved by Y.Nitanai, K.Kakoi, K.Aoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.637, 36.425, 65.728, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / n/a

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala (pdb code 1fvm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala, PDB code: 1fvm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 1fvm

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Chlorine binding site 1 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2

b:8.1
occ:1.00
 CL A:OMZ2 0.0 8.1 1.0
CE1 A:OMZ2 1.7 4.1 1.0
CD1 A:OMZ2 2.7 4.0 1.0
CZ A:OMZ2 2.7 4.8 1.0
OH A:OMZ2 3.0 5.0 1.0
C5 A:GHP4 3.4 4.0 1.0
C6 A:GHP4 3.5 4.6 1.0
CD2 B:OMY6 3.5 6.2 1.0
O A:HOH2004 3.6 35.7 1.0
CE2 B:OMY6 3.6 5.6 1.0
O A:HOH2006 3.7 21.1 1.0
O A:HOH2002 3.7 40.6 1.0
O A:HOH2013 3.7 21.2 1.0
O6 A:BGC8 4.0 10.7 1.0
CG A:OMZ2 4.0 3.7 1.0
CE2 A:OMZ2 4.0 4.6 1.0
O5 A:BGC8 4.2 5.9 1.0
C6 A:BGC8 4.4 7.8 1.0
C4 A:GHP4 4.4 4.7 1.0
CD2 A:OMZ2 4.5 3.8 1.0
C1 A:GHP4 4.6 4.7 1.0
CG B:OMY6 4.6 5.2 1.0
CZ B:OMY6 4.8 5.2 1.0
ODE B:OMY6 4.8 4.2 1.0
O A:ASN3 4.8 5.9 1.0
O4 A:GHP4 4.9 5.8 1.0

Chlorine binding site 2 out of 12 in 1fvm

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Chlorine binding site 2 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl6

b:5.8
occ:1.00
 CL A:OMY6 0.0 5.8 1.0
CE1 A:OMY6 1.8 4.2 1.0
CD1 A:OMY6 2.7 2.9 1.0
CZ A:OMY6 2.8 3.8 1.0
OCZ A:OMY6 3.1 3.3 1.0
C3 A:GHP4 3.1 4.4 1.0
C2 A:GHP4 3.4 4.1 1.0
C5 A:RER9 3.6 4.8 1.0
CB G:DAL3 3.7 5.0 1.0
C4 A:GHP4 3.7 4.7 1.0
C4 A:RER9 3.7 4.9 1.0
C G:DAL2 3.8 5.0 1.0
C5A A:RER9 3.9 4.9 1.0
C3A A:RER9 3.9 3.6 1.0
N G:DAL3 3.9 3.9 1.0
CG A:OMY6 4.0 2.2 1.0
CE2 A:OMY6 4.0 3.2 1.0
CA G:DAL2 4.1 4.2 1.0
O G:DAL2 4.1 8.1 1.0
O1 G:DLS1 4.2 6.0 1.0
O4 A:GHP4 4.2 5.8 1.0
C1 A:GHP4 4.2 4.7 1.0
N G:DAL2 4.2 4.9 1.0
CA G:DAL3 4.4 4.6 1.0
C5 A:GHP4 4.5 4.0 1.0
C3 A:RER9 4.5 5.2 1.0
O A:GHP4 4.5 1.3 1.0
O G:DLS1 4.5 4.9 1.0
C G:DLS1 4.5 4.5 1.0
CD2 A:OMY6 4.5 3.2 1.0
C6 A:GHP4 4.7 4.6 1.0
C A:GHP4 4.7 2.6 1.0
O5 A:RER9 5.0 3.9 1.0

Chlorine binding site 3 out of 12 in 1fvm

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Chlorine binding site 3 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:7.2
occ:1.00
 CL B:OMZ2 0.0 7.2 1.0
CE1 B:OMZ2 1.7 5.1 1.0
CD1 B:OMZ2 2.7 5.7 1.0
CZ B:OMZ2 2.7 6.3 1.0
OH B:OMZ2 3.0 6.6 1.0
C5 B:GHP4 3.3 6.0 1.0
C6 B:GHP4 3.3 5.7 1.0
C5A B:RER9 3.7 9.0 1.0
C5 B:RER9 3.7 8.8 1.0
CD2 A:OMY6 3.8 3.2 1.0
C4 B:RER9 3.8 10.1 1.0
CE2 A:OMY6 3.9 3.2 1.0
CG B:OMZ2 4.0 6.9 1.0
CE2 B:OMZ2 4.0 6.5 1.0
C3A B:RER9 4.1 12.3 1.0
C4 B:GHP4 4.3 6.9 1.0
C1 B:GHP4 4.3 4.1 1.0
O B:ASN3 4.5 4.8 1.0
CD2 B:OMZ2 4.5 7.6 1.0
C3 B:RER9 4.6 11.6 1.0
C B:ASN3 4.7 3.6 1.0
O4 B:GHP4 4.9 6.4 1.0
N B:GHP4 4.9 2.6 1.0
N B:ASN3 4.9 3.8 1.0
O B:OMZ2 4.9 4.8 1.0
CG A:OMY6 4.9 2.2 1.0
C B:OMZ2 5.0 5.5 1.0

Chlorine binding site 4 out of 12 in 1fvm

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Chlorine binding site 4 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:9.8
occ:1.00
 CL B:OMY6 0.0 9.8 1.0
CE1 B:OMY6 1.8 6.1 1.0
CD1 B:OMY6 2.7 4.7 1.0
CZ B:OMY6 2.8 5.2 1.0
C3 B:GHP4 3.1 6.2 1.0
OCZ B:OMY6 3.1 6.2 1.0
O5 B:BGC8 3.2 13.0 1.0
C2 B:GHP4 3.3 5.5 1.0
C6 B:BGC8 3.5 16.2 1.0
CB H:DAL3 3.6 9.5 1.0
C4 B:GHP4 3.6 6.9 1.0
C H:DAL2 3.7 8.3 1.0
C5 B:BGC8 3.8 15.8 1.0
N H:DAL3 3.8 8.1 1.0
CG B:OMY6 4.0 5.2 1.0
CA H:DAL2 4.0 9.3 1.0
O H:DAL2 4.0 9.6 1.0
CE2 B:OMY6 4.0 5.6 1.0
C1 B:GHP4 4.0 4.1 1.0
C1 B:BGC8 4.1 10.3 1.0
O1 H:DLS1 4.1 14.7 1.0
O4 B:GHP4 4.2 6.4 1.0
O6 B:BGC8 4.2 19.1 1.0
O B:GHP4 4.3 4.1 1.0
CA H:DAL3 4.3 8.4 1.0
N H:DAL2 4.3 9.8 1.0
C5 B:GHP4 4.3 6.0 1.0
C6 B:GHP4 4.5 5.7 1.0
CD2 B:OMY6 4.5 6.2 1.0
C H:DLS1 4.6 10.6 1.0
O H:DLS1 4.6 6.0 1.0
C B:GHP4 4.6 3.0 1.0
CA B:GHP4 5.0 3.6 1.0

Chlorine binding site 5 out of 12 in 1fvm

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Chlorine binding site 5 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2

b:8.6
occ:1.00
 CL C:OMZ2 0.0 8.6 1.0
CE1 C:OMZ2 1.7 5.6 1.0
CZ C:OMZ2 2.7 6.2 1.0
CD1 C:OMZ2 2.7 6.7 1.0
OH C:OMZ2 3.0 6.3 1.0
CD2 D:OMY6 3.4 4.8 1.0
C5 C:GHP4 3.5 4.4 1.0
C6 C:GHP4 3.6 4.2 1.0
ODE D:OMY6 3.8 3.6 1.0
O C:HOH2011 3.8 7.9 1.0
O D:HOH2009 3.9 14.4 1.0
CE2 C:OMZ2 4.0 6.5 1.0
CG C:OMZ2 4.0 6.1 1.0
CE2 D:OMY6 4.1 5.0 1.0
CG D:OMY6 4.2 4.2 1.0
O6 C:BGC8 4.3 9.0 1.0
O5 C:BGC8 4.3 6.5 1.0
C6 C:BGC8 4.5 7.4 1.0
CD2 C:OMZ2 4.5 6.4 1.0
CB D:OMY6 4.5 4.9 1.0
C4 C:GHP4 4.6 4.8 1.0
C1 C:GHP4 4.7 4.7 1.0
O C:ASN3 4.7 7.2 1.0

Chlorine binding site 6 out of 12 in 1fvm

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Chlorine binding site 6 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl6

b:6.6
occ:1.00
 CL C:OMY6 0.0 6.6 1.0
CE1 C:OMY6 1.8 5.5 1.0
CD1 C:OMY6 2.7 4.1 1.0
CZ C:OMY6 2.7 4.8 1.0
OCZ C:OMY6 3.0 5.6 1.0
C3 C:GHP4 3.2 4.6 1.0
C2 C:GHP4 3.5 3.1 1.0
C3A C:RER9 3.7 5.5 1.0
CB I:DAL3 3.8 8.3 1.0
O1 I:DLS1 4.0 21.7 1.0
N I:DAL3 4.0 8.7 1.0
C I:DAL2 4.0 11.1 1.0
C4 C:GHP4 4.0 4.8 1.0
CG C:OMY6 4.0 4.4 1.0
CE2 C:OMY6 4.0 3.8 1.0
N I:DAL2 4.2 13.0 1.0
CA I:DAL2 4.2 11.2 1.0
C I:DLS1 4.4 15.3 1.0
O I:DAL2 4.4 11.2 1.0
C5 C:RER9 4.4 6.1 1.0
C1 C:GHP4 4.4 4.7 1.0
O I:DLS1 4.5 11.2 1.0
O C:GHP4 4.5 5.7 1.0
C4 C:RER9 4.5 6.8 1.0
O4 C:GHP4 4.5 5.2 1.0
CA I:DAL3 4.5 8.4 1.0
CD2 C:OMY6 4.5 3.9 1.0
C1 I:DLS1 4.6 20.6 1.0
C3 C:RER9 4.8 6.4 1.0
C5 C:GHP4 4.8 4.4 1.0
C C:GHP4 4.8 4.6 1.0
C5A C:RER9 4.9 5.2 1.0

Chlorine binding site 7 out of 12 in 1fvm

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Chlorine binding site 7 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


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 Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2

b:6.6
occ:1.00
 CL D:OMZ2 0.0 6.6 1.0
CE1 D:OMZ2 1.7 4.5 1.0
CD1 D:OMZ2 2.7 4.1 1.0
CZ D:OMZ2 2.7 4.5 1.0
OH D:OMZ2 3.0 4.5 1.0
C5 D:GHP4 3.4 3.7 1.0
C6 D:GHP4 3.4 2.7 1.0
O C:HOH2003 3.5 4.8 1.0
CD2 C:OMY6 3.6 3.9 1.0
C3A D:RER9 3.8 4.6 1.0
CE2 D:OMZ2 4.0 4.8 1.0
CG D:OMZ2 4.0 3.2 1.0
ODE C:OMY6 4.0 4.0 1.0
C4 D:RER9 4.1 5.5 1.0
CE2 C:OMY6 4.2 3.8 1.0
C5 D:RER9 4.3 5.9 1.0
C4 D:GHP4 4.4 4.4 1.0
CG C:OMY6 4.5 4.4 1.0
CD2 D:OMZ2 4.5 4.6 1.0
C1 D:GHP4 4.5 3.6 1.0
O D:HOH2005 4.6 6.8 1.0
O D:ASN3 4.6 3.8 1.0
C3 D:RER9 4.6 6.3 1.0
C5A D:RER9 4.7 4.7 1.0
CB C:OMY6 4.8 4.4 1.0
O D:OMZ2 4.9 4.0 1.0
C D:ASN3 5.0 3.7 1.0

Chlorine binding site 8 out of 12 in 1fvm

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Chlorine binding site 8 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl6

b:7.3
occ:1.00
 CL D:OMY6 0.0 7.3 1.0
CE1 D:OMY6 1.8 5.3 1.0
CD1 D:OMY6 2.7 4.7 1.0
CZ D:OMY6 2.7 4.4 1.0
OCZ D:OMY6 3.1 6.3 1.0
C3 D:GHP4 3.2 4.8 1.0
O5 D:BGC8 3.4 6.5 1.0
C2 D:GHP4 3.4 3.3 1.0
C6 D:BGC8 3.4 10.5 1.0
O1 J:DLS1 3.6 11.8 1.0
C J:DAL2 3.6 5.2 1.0
CB J:DAL3 3.7 2.5 1.0
O J:HOH2001 3.8 20.7 1.0
N J:DAL3 3.8 4.9 1.0
CA J:DAL2 3.8 4.2 1.0
C4 D:GHP4 3.9 4.4 1.0
C5 D:BGC8 3.9 8.0 1.0
O6 D:BGC8 3.9 14.1 1.0
O J:DAL2 4.0 5.2 1.0
N J:DAL2 4.0 4.7 1.0
CG D:OMY6 4.0 4.2 1.0
CE2 D:OMY6 4.0 5.0 1.0
C1 J:DLS1 4.1 10.0 1.0
C J:DLS1 4.2 4.0 1.0
O D:GHP4 4.2 3.0 1.0
C1 D:GHP4 4.3 3.6 1.0
O J:DLS1 4.3 3.9 1.0
C1 D:BGC8 4.3 5.3 1.0
CA J:DAL3 4.4 4.0 1.0
O4 D:GHP4 4.4 6.3 1.0
CD2 D:OMY6 4.5 4.8 1.0
C2 J:DLS1 4.6 11.7 1.0
C D:GHP4 4.6 3.7 1.0
C5 D:GHP4 4.6 3.7 1.0
N J:DLS1 4.7 7.7 1.0
C6 D:GHP4 4.8 2.7 1.0
CA J:DLS1 5.0 6.0 1.0

Chlorine binding site 9 out of 12 in 1fvm

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Chlorine binding site 9 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl2

b:6.8
occ:1.00
 CL E:OMZ2 0.0 6.8 1.0
CE1 E:OMZ2 1.8 4.5 1.0
CD1 E:OMZ2 2.7 5.4 1.0
CZ E:OMZ2 2.7 4.2 1.0
OH E:OMZ2 3.0 4.6 1.0
ODE F:OMY6 3.1 3.3 1.0
C6 E:GHP4 3.3 3.2 1.0
C5 E:GHP4 3.3 4.1 1.0
O E:HOH2018 3.8 18.4 1.0
CD2 F:OMY6 4.0 3.7 1.0
CE2 E:OMZ2 4.0 4.6 1.0
O E:ASN3 4.0 3.8 1.0
CG E:OMZ2 4.0 4.5 1.0
O F:HOH2006 4.1 16.6 1.0
O6 E:BGC8 4.1 7.7 1.0
C6 E:BGC8 4.2 7.5 1.0
O5 E:BGC8 4.2 6.1 1.0
CB F:OMY6 4.3 4.1 1.0
O E:HOH2005 4.4 32.3 1.0
C1 E:GHP4 4.4 3.2 1.0
C4 E:GHP4 4.4 4.9 1.0
CD2 E:OMZ2 4.5 5.8 1.0
CG F:OMY6 4.6 3.2 1.0
C E:ASN3 4.6 3.9 1.0
C5 E:BGC8 5.0 7.7 1.0

Chlorine binding site 10 out of 12 in 1fvm

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Chlorine binding site 10 out of 12 in the Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Complex of Vancomycin with Di-Acetyl-Lys-D-Ala-D-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl6

b:5.2
occ:1.00
 CL E:OMY6 0.0 5.2 1.0
CE1 E:OMY6 1.8 3.0 1.0
CD1 E:OMY6 2.7 4.2 1.0
CZ E:OMY6 2.7 3.4 1.0
OCZ E:OMY6 3.0 3.5 1.0
C3 E:GHP4 3.2 4.0 1.0
C2 E:GHP4 3.5 2.5 1.0
O K:HOH2003 3.5 31.6 1.0
C K:DAL2 3.6 7.4 1.0
CB K:DAL3 3.7 7.4 1.0
N K:DAL3 3.8 6.7 1.0
O1 K:DLS1 3.8 10.7 1.0
C3A E:RER9 3.8 6.1 1.0
CA K:DAL2 3.9 5.6 1.0
N K:DAL2 3.9 7.2 1.0
C5 E:RER9 3.9 5.9 1.0
C4 E:GHP4 3.9 4.9 1.0
C4 E:RER9 4.0 6.7 1.0
O K:DAL2 4.0 6.1 1.0
CG E:OMY6 4.0 3.5 1.0
CE2 E:OMY6 4.0 4.1 1.0
C5A E:RER9 4.2 5.7 1.0
C K:DLS1 4.2 8.9 1.0
CA K:DAL3 4.3 6.7 1.0
O E:GHP4 4.4 5.1 1.0
C1 E:GHP4 4.4 3.2 1.0
C1 K:DLS1 4.4 11.2 1.0
O4 E:GHP4 4.4 5.0 1.0
O K:DLS1 4.4 8.3 1.0
CD2 E:OMY6 4.5 4.4 1.0
C3 E:RER9 4.6 7.9 1.0
C5 E:GHP4 4.8 4.1 1.0
C E:GHP4 4.8 3.4 1.0
N K:DLS1 4.9 10.3 1.0
C6 E:GHP4 4.9 3.2 1.0
CA K:DLS1 4.9 11.4 1.0

Reference:

Y.Nitanai, T.Kikuchi, K.Kakoi, S.Hanamaki, I.Fujisawa, K.Aoki. Crystal Structures of the Complexes Between Vancomycin and Cell-Wall Precursor Analogs. J.Mol.Biol. V. 385 1422 2009.
ISSN: ISSN 0022-2836
PubMed: 18976660
DOI: 10.1016/J.JMB.2008.10.026
Page generated: Fri Jul 19 22:00:50 2024

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