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Chlorine in PDB 4rpn: Pcpr Inducer Binding Domain Complex with Pentachlorophenol

Protein crystallography data

The structure of Pcpr Inducer Binding Domain Complex with Pentachlorophenol, PDB code: 4rpn was solved by R.P.Hayes, T.W.Moural, K.M.Lewis, D.Onofrei, L.Xun, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.46 / 2.27
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 169.048, 169.048, 110.264, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 21.5

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Chlorine atom in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol (pdb code 4rpn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 40 binding sites of Chlorine where determined in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol, PDB code: 4rpn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 40 in 4rpn

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Chlorine binding site 1 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:40.9
occ:1.00
 CL1 D:PCI401 0.0 40.9 1.0
C2 D:PCI401 1.7 31.2 1.0
C3 D:PCI401 2.7 35.8 1.0
C1 D:PCI401 2.7 30.3 1.0
O1 D:PCI401 3.0 29.3 1.0
CL2 D:PCI401 3.1 47.5 1.0
O D:HOH584 3.2 35.2 1.0
CA D:GLY107 3.4 24.9 1.0
CE2 D:PHE151 3.5 25.6 1.0
N D:GLY107 3.9 22.1 1.0
CZ D:PHE151 3.9 24.9 1.0
C4 D:PCI401 4.0 28.3 1.0
CD2 D:PHE151 4.0 24.6 1.0
C6 D:PCI401 4.0 32.0 1.0
CA D:GLY152 4.1 27.9 1.0
CG1 D:VAL275 4.2 26.0 1.0
CD2 D:PHE106 4.3 21.4 1.0
CD1 D:LEU110 4.3 32.5 1.0
CE2 D:PHE106 4.5 22.4 1.0
OG D:SER104 4.5 25.6 1.0
C5 D:PCI401 4.5 31.4 1.0
CE1 D:PHE151 4.7 24.2 1.0
N D:GLY152 4.7 30.6 1.0
O D:PHE151 4.7 28.4 1.0
CG D:PHE151 4.8 26.3 1.0
C D:GLY107 4.8 23.9 1.0
C D:PHE106 4.8 22.1 1.0
C D:PHE151 4.9 27.8 1.0

Chlorine binding site 2 out of 40 in 4rpn

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Chlorine binding site 2 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:47.5
occ:1.00
 CL2 D:PCI401 0.0 47.5 1.0
C3 D:PCI401 1.7 35.8 1.0
C4 D:PCI401 2.7 28.3 1.0
C2 D:PCI401 2.7 31.2 1.0
CL3 D:PCI401 3.0 37.4 1.0
CL1 D:PCI401 3.1 40.9 1.0
CG2 D:VAL275 3.2 33.0 1.0
CE1 D:PHE167 3.7 30.3 1.0
CE2 D:PHE106 3.7 22.4 1.0
CZ D:PHE167 3.7 34.4 1.0
CG1 D:VAL275 3.8 26.0 1.0
C5 D:PCI401 4.0 31.4 1.0
C1 D:PCI401 4.0 30.3 1.0
CD1 D:LEU110 4.0 32.5 1.0
CB D:VAL275 4.1 29.9 1.0
CZ D:PHE106 4.4 23.8 1.0
CD2 D:PHE106 4.4 21.4 1.0
C6 D:PCI401 4.5 32.0 1.0
CB D:GLU169 4.7 26.1 1.0
CG D:GLU169 4.9 34.8 1.0
CD1 D:PHE167 4.9 35.9 1.0
CE2 D:PHE167 5.0 32.5 1.0

Chlorine binding site 3 out of 40 in 4rpn

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Chlorine binding site 3 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:37.4
occ:1.00
 CL3 D:PCI401 0.0 37.4 1.0
C4 D:PCI401 1.8 28.3 1.0
C3 D:PCI401 2.7 35.8 1.0
C5 D:PCI401 2.8 31.4 1.0
CL2 D:PCI401 3.0 47.5 1.0
CL4 D:PCI401 3.2 35.3 1.0
CG D:GLU169 3.3 34.8 1.0
CB D:GLU169 3.4 26.1 1.0
CG D:PRO248 3.6 24.4 1.0
CB D:PRO248 3.7 25.9 1.0
CG2 D:VAL275 4.0 33.0 1.0
C2 D:PCI401 4.0 31.2 1.0
C6 D:PCI401 4.0 32.0 1.0
CG2 D:ILE273 4.0 34.7 1.0
CB D:ILE273 4.3 34.0 1.0
CE2 D:PHE106 4.4 22.4 1.0
C1 D:PCI401 4.5 30.3 1.0
CD D:GLU169 4.5 31.9 1.0
CG1 D:ILE273 4.6 34.9 1.0
OE2 D:GLU169 4.7 36.5 1.0
CA D:PRO248 4.8 23.5 1.0
CA D:GLU169 4.8 30.3 1.0

Chlorine binding site 4 out of 40 in 4rpn

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Chlorine binding site 4 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:35.3
occ:1.00
 CL4 D:PCI401 0.0 35.3 1.0
C5 D:PCI401 1.7 31.4 1.0
C6 D:PCI401 2.7 32.0 1.0
C4 D:PCI401 2.7 28.3 1.0
OH D:TYR171 3.0 26.2 1.0
CL5 D:PCI401 3.1 35.5 1.0
CL3 D:PCI401 3.2 37.4 1.0
CG D:PRO248 3.8 24.4 1.0
CZ D:TYR171 3.9 27.0 1.0
CB D:HIS208 4.0 26.3 1.0
C1 D:PCI401 4.0 30.3 1.0
CG1 D:VAL207 4.0 33.6 1.0
C3 D:PCI401 4.0 35.8 1.0
CA D:HIS208 4.2 29.2 1.0
N D:HIS208 4.2 27.1 1.0
CE1 D:TYR171 4.3 25.7 1.0
CZ D:PHE231 4.5 23.0 1.0
C2 D:PCI401 4.5 31.2 1.0
ND1 D:HIS208 4.5 25.0 1.0
CD D:PRO248 4.7 20.7 1.0
CG D:HIS208 4.7 25.8 1.0
CG2 D:ILE273 4.8 34.7 1.0
CG1 D:ILE273 4.8 34.9 1.0
C D:VAL207 4.9 30.3 1.0
CE2 D:TYR171 4.9 26.1 1.0
CB D:PRO248 5.0 25.9 1.0

Chlorine binding site 5 out of 40 in 4rpn

Go back to Chlorine Binding Sites List in 4rpn
Chlorine binding site 5 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:35.5
occ:1.00
 CL5 D:PCI401 0.0 35.5 1.0
C6 D:PCI401 1.8 32.0 1.0
C5 D:PCI401 2.7 31.4 1.0
C1 D:PCI401 2.7 30.3 1.0
O1 D:PCI401 3.0 29.3 1.0
CL4 D:PCI401 3.1 35.3 1.0
ND1 D:HIS206 3.2 37.8 1.0
CE2 D:PHE231 3.7 26.8 1.0
CZ D:PHE231 3.8 23.0 1.0
CE1 D:HIS206 3.8 35.4 1.0
CB D:HIS208 3.8 26.3 1.0
C4 D:PCI401 4.0 28.3 1.0
C2 D:PCI401 4.0 31.2 1.0
CG D:HIS206 4.1 36.1 1.0
N D:HIS208 4.2 27.1 1.0
OG D:SER104 4.2 25.6 1.0
CB D:HIS206 4.5 34.7 1.0
C3 D:PCI401 4.5 35.8 1.0
CB D:SER104 4.5 22.6 1.0
CA D:HIS208 4.6 29.2 1.0
CG1 D:VAL207 4.6 33.6 1.0
CD2 D:PHE231 4.8 24.5 1.0
N D:VAL207 4.9 28.7 1.0
CG D:HIS208 4.9 25.8 1.0
NE2 D:HIS206 4.9 41.1 1.0
CE1 D:PHE231 5.0 24.1 1.0

Chlorine binding site 6 out of 40 in 4rpn

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Chlorine binding site 6 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:35.9
occ:1.00
 CL1 D:PCI402 0.0 35.9 1.0
C2 D:PCI402 1.7 27.9 1.0
C3 D:PCI402 2.7 25.9 1.0
C1 D:PCI402 2.7 25.0 1.0
O1 D:PCI402 2.9 34.3 1.0
CL2 D:PCI402 3.0 32.4 1.0
O D:ARG250 3.3 24.4 1.0
O D:HOH526 3.3 38.7 1.0
CD2 D:LEU110 3.5 31.0 1.0
C D:ARG250 3.5 24.2 1.0
O D:HOH504 3.7 27.4 1.0
CE1 D:PHE106 3.8 20.1 1.0
CB D:TRP254 3.9 22.1 1.0
CB D:ARG250 3.9 27.5 1.0
N D:LEU251 3.9 21.9 1.0
C4 D:PCI402 4.0 26.2 1.0
C6 D:PCI402 4.0 30.9 1.0
CG D:LEU110 4.0 31.4 1.0
CA D:LEU251 4.1 22.2 1.0
CA D:ARG250 4.3 23.9 1.0
CZ D:PHE106 4.5 23.8 1.0
C5 D:PCI402 4.5 29.8 1.0
CG D:TRP254 4.5 24.9 1.0
CD1 D:TRP254 4.7 23.9 1.0
CD1 D:PHE106 4.7 23.6 1.0
O D:HOH572 4.8 40.1 1.0
CG D:ARG250 4.9 29.7 1.0
CB D:LEU251 5.0 22.6 1.0

Chlorine binding site 7 out of 40 in 4rpn

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Chlorine binding site 7 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:32.4
occ:1.00
 CL2 D:PCI402 0.0 32.4 1.0
C3 D:PCI402 1.7 25.9 1.0
C2 D:PCI402 2.7 27.9 1.0
C4 D:PCI402 2.7 26.2 1.0
CL1 D:PCI402 3.0 35.9 1.0
CL3 D:PCI402 3.0 29.0 1.0
CD1 D:LEU251 3.2 21.7 1.0
CB D:TRP254 3.6 22.1 1.0
CA D:LEU251 3.7 22.2 1.0
CE1 D:PHE106 3.8 20.1 1.0
CD1 D:PHE106 3.9 23.6 1.0
CG D:TRP254 3.9 24.9 1.0
C1 D:PCI402 3.9 25.0 1.0
C5 D:PCI402 4.0 29.8 1.0
CB D:LEU251 4.1 22.6 1.0
CD2 D:TRP254 4.2 24.3 1.0
CG D:LEU251 4.2 23.7 1.0
O D:LEU251 4.3 26.2 1.0
CE3 D:TRP254 4.4 24.5 1.0
C6 D:PCI402 4.5 30.9 1.0
C D:LEU251 4.6 24.0 1.0
CD1 D:TRP254 4.6 23.9 1.0
N D:LEU251 4.6 21.9 1.0
O D:ARG250 4.6 24.4 1.0
CD2 D:LEU232 4.7 26.2 1.0
CE2 D:PHE255 4.8 26.0 1.0
CD2 D:PHE255 4.9 25.4 1.0
C D:ARG250 4.9 24.2 1.0
CB D:ALA109 5.0 25.3 1.0

Chlorine binding site 8 out of 40 in 4rpn

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Chlorine binding site 8 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:29.0
occ:1.00
 CL3 D:PCI402 0.0 29.0 1.0
C4 D:PCI402 1.7 26.2 1.0
C3 D:PCI402 2.7 25.9 1.0
C5 D:PCI402 2.8 29.8 1.0
CL2 D:PCI402 3.0 32.4 1.0
CL4 D:PCI402 3.2 31.1 1.0
CG2 C:VAL236 3.4 20.7 1.0
CB C:VAL236 3.6 26.9 1.0
CD2 D:TRP254 3.6 24.3 1.0
CE2 D:TRP254 3.7 26.7 1.0
CB D:ALA109 3.7 25.3 1.0
CE3 D:TRP254 3.8 24.5 1.0
CG1 C:VAL236 3.9 23.4 1.0
CZ2 D:TRP254 3.9 27.9 1.0
C2 D:PCI402 4.0 27.9 1.0
CZ3 D:TRP254 4.0 24.4 1.0
C6 D:PCI402 4.0 30.9 1.0
CH2 D:TRP254 4.1 29.1 1.0
CG D:TRP254 4.1 24.9 1.0
CD2 D:LEU232 4.2 26.2 1.0
NE1 D:TRP254 4.2 23.8 1.0
CD1 D:TRP254 4.5 23.9 1.0
C1 D:PCI402 4.5 25.0 1.0
CB D:TRP254 4.9 22.1 1.0
CE2 D:PHE255 4.9 26.0 1.0
CA D:ALA109 4.9 22.1 1.0

Chlorine binding site 9 out of 40 in 4rpn

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Chlorine binding site 9 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:31.1
occ:1.00
 CL4 D:PCI402 0.0 31.1 1.0
C5 D:PCI402 1.7 29.8 1.0
C4 D:PCI402 2.7 26.2 1.0
C6 D:PCI402 2.7 30.9 1.0
CL5 D:PCI402 3.1 35.3 1.0
CL3 D:PCI402 3.2 29.0 1.0
CG C:GLU240 3.3 24.7 1.0
CG2 C:VAL236 3.5 20.7 1.0
O C:VAL236 3.6 25.3 1.0
NE1 D:TRP254 3.7 23.8 1.0
O D:ALA109 3.7 23.9 1.0
CB C:VAL236 3.7 26.9 1.0
C C:VAL236 3.9 23.9 1.0
CE2 D:TRP254 3.9 26.7 1.0
C3 D:PCI402 4.0 25.9 1.0
C1 D:PCI402 4.0 25.0 1.0
CZ2 D:TRP254 4.1 27.9 1.0
CG D:PRO113 4.2 21.8 1.0
CD C:GLU240 4.2 32.5 1.0
OE2 C:GLU240 4.3 38.4 1.0
CD1 D:TRP254 4.4 23.9 1.0
CB C:GLU240 4.4 25.8 1.0
CA C:VAL236 4.4 24.4 1.0
CB D:ALA109 4.5 25.3 1.0
C D:ALA109 4.5 24.3 1.0
C2 D:PCI402 4.5 27.9 1.0
N C:ILE237 4.5 23.0 1.0
CA D:ALA109 4.8 22.1 1.0
CD2 D:TRP254 4.8 24.3 1.0
CA C:ILE237 4.9 20.7 1.0
CG1 C:VAL236 5.0 23.4 1.0

Chlorine binding site 10 out of 40 in 4rpn

Go back to Chlorine Binding Sites List in 4rpn
Chlorine binding site 10 out of 40 in the Pcpr Inducer Binding Domain Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Pcpr Inducer Binding Domain Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:35.3
occ:1.00
 CL5 D:PCI402 0.0 35.3 1.0
C6 D:PCI402 1.7 30.9 1.0
C5 D:PCI402 2.7 29.8 1.0
C1 D:PCI402 2.7 25.0 1.0
O1 D:PCI402 3.0 34.3 1.0
CL4 D:PCI402 3.1 31.1 1.0
NH1 D:ARG114 3.4 32.2 1.0
CG C:GLU240 3.6 24.7 1.0
CG D:PRO305 3.7 51.0 1.0
O D:HOH572 3.8 40.1 1.0
O D:ALA109 3.8 23.9 1.0
CG D:PRO113 3.9 21.8 1.0
CD C:GLU240 3.9 32.5 1.0
CB D:PRO113 3.9 23.1 1.0
C2 D:PCI402 4.0 27.9 1.0
C4 D:PCI402 4.0 26.2 1.0
CD D:PRO305 4.1 53.8 1.0
OE1 C:GLU240 4.2 33.4 1.0
OE2 C:GLU240 4.4 38.4 1.0
NE1 D:TRP254 4.4 23.8 1.0
CZ D:ARG114 4.4 38.1 1.0
CB C:GLU240 4.5 25.8 1.0
CD1 D:TRP254 4.5 23.9 1.0
C3 D:PCI402 4.5 25.9 1.0
NH2 D:ARG114 4.7 39.6 1.0
O D:LEU110 4.8 24.0 1.0
C D:ALA109 4.8 24.3 1.0
CD D:PRO113 4.9 25.1 1.0
CA D:LEU110 5.0 25.3 1.0

Reference:

R.P.Hayes, T.W.Moural, K.M.Lewis, D.Onofrei, L.Xun, C.Kang. Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator Pcpr From Sphingobium Chlorophenolicum. Int J Mol Sci V. 15 20736 2014.
ISSN: ESSN 1422-0067
PubMed: 25397598
DOI: 10.3390/IJMS151120736
Page generated: Fri Jul 11 21:26:42 2025

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