Chlorine in PDB 4rpo: Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)

The structure of Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol), PDB code: 4rpo 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)	49.61 / 1.95
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	169.751, 169.751, 110.115, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.9

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol) (pdb code 4rpo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol), PDB code: 4rpo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:44.4 occ:1.00 CL2 A:T6C401 0.0 44.4 1.0 C2 A:T6C401 1.7 37.4 1.0 C3 A:T6C401 2.7 30.9 1.0 C1 A:T6C401 2.7 27.0 1.0 O1 A:T6C401 3.0 30.0 1.0 CZ A:PHE231 3.3 26.0 1.0 CE1 A:PHE231 3.4 31.0 1.0 CE1 A:HIS206 3.6 32.1 1.0 NE2 A:HIS206 3.7 31.7 1.0 CE2 A:PHE231 3.9 24.3 1.0 OG A:SER104 3.9 23.8 1.0 CG A:PRO248 3.9 31.7 1.0 C4 A:T6C401 4.0 29.8 1.0 C6 A:T6C401 4.0 28.4 1.0 CD1 A:PHE231 4.1 24.2 1.0 CD2 A:PHE231 4.5 25.3 1.0 C5 A:T6C401 4.5 23.9 1.0 CG A:PHE231 4.6 21.9 1.0 CB A:SER104 4.6 20.6 1.0 ND1 A:HIS206 4.7 29.6 1.0 CD2 A:PHE106 4.7 26.9 1.0 CD A:PRO248 4.7 27.4 1.0 CD2 A:HIS206 4.9 33.2 1.0

Chlorine binding site 2 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:35.5 occ:1.00 CL6 A:T6C401 0.0 35.5 1.0 C6 A:T6C401 1.7 28.4 1.0 C1 A:T6C401 2.7 27.0 1.0 C5 A:T6C401 2.7 23.9 1.0 O1 A:T6C401 3.0 30.0 1.0 CE2 A:PHE151 3.3 22.5 1.0 CD2 A:PHE151 3.4 23.0 1.0 O A:HOH505 3.4 25.2 1.0 CA A:GLY107 3.5 20.6 1.0 CA A:GLY152 3.5 26.5 1.0 O A:PHE151 3.6 22.7 1.0 CZ A:PHE151 3.8 23.3 1.0 N A:GLY152 3.9 24.2 1.0 C A:PHE151 3.9 25.5 1.0 C4 A:T6C401 4.0 29.8 1.0 C2 A:T6C401 4.0 37.4 1.0 CG A:PHE151 4.0 21.4 1.0 CG1 A:VAL275 4.0 23.1 1.0 CE1 A:PHE151 4.4 24.2 1.0 N A:GLY107 4.4 19.3 1.0 CD1 A:PHE151 4.4 23.2 1.0 C3 A:T6C401 4.5 30.9 1.0 C A:GLY107 4.6 21.0 1.0 OG A:SER104 4.7 23.8 1.0 CB A:PHE151 4.8 23.9 1.0 C A:GLY152 4.8 24.4 1.0 O A:GLY107 4.9 21.8 1.0 CB A:ALA103 4.9 18.4 1.0 CG2 A:VAL275 4.9 24.7 1.0 CA A:PHE151 4.9 20.6 1.0

Chlorine binding site 3 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:34.5 occ:1.00 CL4 A:T6C401 0.0 34.5 1.0 C4 A:T6C401 1.7 29.8 1.0 C3 A:T6C401 2.7 30.9 1.0 C5 A:T6C401 2.7 23.9 1.0 OE2 A:GLU169 3.5 32.5 1.0 CE1 A:PHE167 3.6 24.7 1.0 CE2 A:PHE106 3.7 28.7 1.0 CZ A:PHE167 3.8 25.0 1.0 CG A:GLU169 3.9 30.0 1.0 C2 A:T6C401 3.9 37.4 1.0 C6 A:T6C401 4.0 28.4 1.0 CD A:ARG250 4.0 39.2 1.0 CD A:GLU169 4.0 33.5 1.0 CD2 A:LEU110 4.2 22.0 1.0 CB A:PRO248 4.2 29.7 1.0 CB A:GLU169 4.3 29.9 1.0 CD2 A:PHE106 4.3 26.9 1.0 CG2 A:VAL275 4.3 24.7 1.0 CB A:ARG250 4.4 28.5 1.0 C1 A:T6C401 4.5 27.0 1.0 NE A:ARG250 4.7 41.5 1.0 CZ A:PHE106 4.7 24.4 1.0 CG A:PRO248 4.8 31.7 1.0 CG A:ARG250 4.8 34.8 1.0 CD1 A:PHE167 4.9 24.0 1.0

Chlorine binding site 4 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:47.3 occ:1.00 CL2 B:T6C401 0.0 47.3 1.0 C2 B:T6C401 1.7 33.3 1.0 C1 B:T6C401 2.7 32.2 1.0 C3 B:T6C401 2.7 30.1 1.0 O1 B:T6C401 2.9 32.2 1.0 CZ B:PHE231 3.3 29.2 1.0 CE2 B:PHE231 3.4 31.9 1.0 CE1 B:HIS206 3.4 35.8 1.0 NE2 B:HIS206 3.6 31.8 1.0 CE1 B:PHE231 3.8 29.4 1.0 OG B:SER104 3.9 24.6 1.0 C6 B:T6C401 4.0 28.5 1.0 C4 B:T6C401 4.0 31.0 1.0 CG B:PRO248 4.0 32.4 1.0 CD2 B:PHE231 4.1 28.6 1.0 CD1 B:PHE231 4.4 25.6 1.0 C5 B:T6C401 4.5 28.2 1.0 CG B:PHE231 4.5 24.3 1.0 ND1 B:HIS206 4.5 32.1 1.0 CB B:SER104 4.6 20.8 1.0 CD2 B:PHE106 4.8 29.2 1.0 CD2 B:HIS206 4.8 33.3 1.0 CD B:PRO248 4.9 26.3 1.0

Chlorine binding site 5 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:37.7 occ:1.00 CL6 B:T6C401 0.0 37.7 1.0 C6 B:T6C401 1.7 28.5 1.0 C5 B:T6C401 2.7 28.2 1.0 C1 B:T6C401 2.7 32.2 1.0 O1 B:T6C401 3.0 32.2 1.0 CE2 B:PHE151 3.4 25.4 1.0 O B:HOH502 3.4 28.1 1.0 CD2 B:PHE151 3.4 25.2 1.0 CA B:GLY107 3.5 21.6 1.0 O B:PHE151 3.5 26.2 1.0 CA B:GLY152 3.6 25.6 1.0 CZ B:PHE151 3.8 24.3 1.0 C B:PHE151 3.8 25.3 1.0 N B:GLY152 3.8 22.4 1.0 CG1 B:VAL275 3.9 24.1 1.0 CG B:PHE151 3.9 23.6 1.0 C4 B:T6C401 4.0 31.0 1.0 C2 B:T6C401 4.0 33.3 1.0 CE1 B:PHE151 4.3 24.8 1.0 CD1 B:PHE151 4.3 25.4 1.0 N B:GLY107 4.4 21.8 1.0 C3 B:T6C401 4.5 30.1 1.0 C B:GLY107 4.6 22.8 1.0 OG B:SER104 4.7 24.6 1.0 CB B:PHE151 4.8 22.5 1.0 C B:GLY152 4.8 28.2 1.0 O B:GLY107 4.8 21.0 1.0 CB B:ALA103 4.9 24.1 1.0 CA B:PHE151 4.9 25.9 1.0 CG2 B:VAL275 5.0 25.5 1.0

Chlorine binding site 6 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:37.1 occ:1.00 CL4 B:T6C401 0.0 37.1 1.0 C4 B:T6C401 1.7 31.0 1.0 C3 B:T6C401 2.7 30.1 1.0 C5 B:T6C401 2.7 28.2 1.0 OE1 B:GLU169 3.3 34.9 1.0 CE1 B:PHE167 3.5 29.1 1.0 CE2 B:PHE106 3.7 28.6 1.0 CG B:GLU169 3.8 33.7 1.0 CD B:ARG250 3.9 31.9 0.8 CZ B:PHE167 3.9 22.9 1.0 CD B:GLU169 4.0 33.9 1.0 C2 B:T6C401 4.0 33.3 1.0 C6 B:T6C401 4.0 28.5 1.0 CD B:ARG250 4.2 31.9 0.2 CB B:PRO248 4.2 29.4 1.0 CB B:GLU169 4.2 32.1 1.0 CD2 B:PHE106 4.3 29.2 1.0 CB B:ARG250 4.3 29.8 0.2 CD2 B:LEU110 4.3 26.2 1.0 CG2 B:VAL275 4.4 25.5 1.0 CB B:ARG250 4.4 29.7 0.8 C1 B:T6C401 4.5 32.2 1.0 NE B:ARG250 4.5 33.4 0.8 CG B:ARG250 4.6 32.4 0.2 CG B:ARG250 4.8 32.6 0.8 CD1 B:PHE167 4.8 29.3 1.0 CZ B:PHE106 4.8 26.2 1.0 CG B:PRO248 4.8 32.4 1.0

Chlorine binding site 7 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:49.5 occ:1.00 CL2 C:T6C401 0.0 49.5 1.0 C2 C:T6C401 1.7 36.2 1.0 C3 C:T6C401 2.7 35.8 1.0 C1 C:T6C401 2.7 34.1 1.0 O1 C:T6C401 2.9 32.2 1.0 CZ C:PHE231 3.3 31.3 1.0 CE1 C:HIS206 3.4 40.0 1.0 CE1 C:PHE231 3.4 31.8 1.0 NE2 C:HIS206 3.6 41.9 1.0 CE2 C:PHE231 4.0 30.3 1.0 C4 C:T6C401 4.0 33.7 1.0 C6 C:T6C401 4.0 32.4 1.0 CG C:PRO248 4.0 31.4 1.0 OG C:SER104 4.0 28.9 1.0 CD1 C:PHE231 4.2 31.9 1.0 CD2 C:PHE106 4.4 29.0 1.0 C5 C:T6C401 4.5 33.0 1.0 ND1 C:HIS206 4.5 37.2 1.0 CD2 C:PHE231 4.6 25.6 1.0 OH C:TYR171 4.6 35.9 1.0 CG C:PHE231 4.7 27.8 1.0 CB C:SER104 4.8 25.2 1.0 CD C:PRO248 4.8 27.1 1.0 CD2 C:HIS206 4.8 41.7 1.0 CB C:HIS208 5.0 29.1 1.0

Chlorine binding site 8 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:41.4 occ:1.00 CL6 C:T6C401 0.0 41.4 1.0 C6 C:T6C401 1.7 32.4 1.0 C5 C:T6C401 2.7 33.0 1.0 C1 C:T6C401 2.7 34.1 1.0 O1 C:T6C401 3.0 32.2 1.0 O C:HOH501 3.4 29.4 1.0 CE2 C:PHE151 3.4 30.2 1.0 CD2 C:PHE151 3.4 31.9 1.0 CA C:GLY107 3.5 28.4 1.0 CA C:GLY152 3.5 34.3 1.0 O C:PHE151 3.5 28.6 1.0 N C:GLY152 3.8 32.1 1.0 C C:PHE151 3.8 35.6 1.0 CZ C:PHE151 3.9 31.0 1.0 CG1 C:VAL275 3.9 33.0 1.0 CG C:PHE151 4.0 30.9 1.0 C4 C:T6C401 4.0 33.7 1.0 C2 C:T6C401 4.0 36.2 1.0 CE1 C:PHE151 4.3 31.1 1.0 N C:GLY107 4.4 25.4 1.0 CD1 C:PHE151 4.4 32.8 1.0 C3 C:T6C401 4.5 35.8 1.0 C C:GLY107 4.6 25.1 1.0 OG C:SER104 4.6 28.9 1.0 CB C:PHE151 4.8 30.3 1.0 C C:GLY152 4.8 35.5 1.0 CB C:ALA103 4.8 25.1 1.0 O C:GLY107 4.9 26.9 1.0 CA C:PHE151 4.9 30.5 1.0

Chlorine binding site 9 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:40.9 occ:1.00 CL4 C:T6C401 0.0 40.9 1.0 C4 C:T6C401 1.7 33.7 1.0 C3 C:T6C401 2.7 35.8 1.0 C5 C:T6C401 2.7 33.0 1.0 OE2 C:GLU169 3.5 38.5 1.0 CE2 C:PHE167 3.6 38.0 1.0 CE2 C:PHE106 3.7 31.5 1.0 CG C:GLU169 3.8 38.1 1.0 CZ C:PHE167 3.9 37.0 1.0 C2 C:T6C401 3.9 36.2 1.0 C6 C:T6C401 4.0 32.4 1.0 CD C:ARG250 4.0 42.0 1.0 CD C:GLU169 4.0 36.5 1.0 CB C:GLU169 4.1 36.5 1.0 CG2 C:VAL275 4.1 34.9 1.0 CD2 C:LEU110 4.3 29.6 1.0 CB C:PRO248 4.3 30.5 1.0 CD2 C:PHE106 4.4 29.0 1.0 C1 C:T6C401 4.5 34.1 1.0 CB C:ARG250 4.5 33.8 1.0 CZ C:PHE106 4.6 27.5 1.0 NH1 C:ARG250 4.8 46.3 1.0 CG C:ARG250 4.8 39.9 1.0 CD2 C:PHE167 4.8 38.5 1.0 CG C:PRO248 4.9 31.4 1.0 NE C:ARG250 5.0 47.5 1.0

Chlorine binding site 10 out of 12 in the Pcpr Inducer Binding Domain (Complex with 2,4,6-Trichlorophenol)


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 2,4,6-Trichlorophenol) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl402 b:47.7 occ:1.00 CL2 D:T6C402 0.0 47.7 1.0 C2 D:T6C402 1.7 36.5 1.0 C1 D:T6C402 2.7 32.4 1.0 C3 D:T6C402 2.7 34.2 1.0 O1 D:T6C402 2.9 32.5 1.0 CZ D:PHE231 3.3 27.9 1.0 CE2 D:PHE231 3.4 29.2 1.0 CE1 D:HIS206 3.4 35.5 1.0 NE2 D:HIS206 3.7 30.9 1.0 OG D:SER104 3.9 27.7 1.0 CE1 D:PHE231 3.9 26.4 1.0 C6 D:T6C402 4.0 30.8 1.0 C4 D:T6C402 4.0 33.4 1.0 CG D:PRO248 4.0 30.6 1.0 CD2 D:PHE231 4.1 24.2 1.0 C5 D:T6C402 4.5 31.7 1.0 ND1 D:HIS206 4.5 29.9 1.0 CD1 D:PHE231 4.6 24.6 1.0 CG D:PHE231 4.6 23.9 1.0 CB D:SER104 4.7 24.4 1.0 CD2 D:PHE106 4.7 26.6 1.0 CD D:PRO248 4.8 25.5 1.0 CD2 D:HIS206 4.9 32.9 1.0 CB D:PRO248 5.0 23.4 1.0

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