Chlorine in PDB 6onk: Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol

The structure of Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol, PDB code: 6onk was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.234, 68.025, 66.761, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 18.3

The structure of Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol (pdb code 6onk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol, PDB code: 6onk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:21.6 occ:0.58 CL1 A:MZG202 0.0 21.6 0.6 C1 A:MZG202 0.6 13.8 0.2 C2 A:MZG202 1.6 13.2 0.2 C6 A:MZG202 1.7 16.4 0.6 C3 A:MZG202 2.5 13.3 0.2 C7 A:MZG202 2.7 12.3 0.2 C7 A:MZG202 2.7 18.7 0.6 C5 A:MZG202 2.7 16.3 0.6 O1 A:MZG202 2.7 16.9 0.2 C2C A:HEM201 3.2 14.9 1.0 C1C A:HEM201 3.3 16.4 1.0 C3C A:HEM201 3.6 15.1 1.0 NC A:HEM201 3.7 17.1 1.0 CMC A:HEM201 3.7 17.5 1.0 CD2 A:LEU100 3.7 17.5 1.0 CHC A:HEM201 3.8 15.6 1.0 C4 A:MZG202 3.8 13.1 0.2 C6 A:MZG202 3.9 11.8 0.2 C4C A:HEM201 3.9 18.5 1.0 C4 A:MZG202 3.9 15.7 0.6 C2 A:MZG202 4.0 16.8 0.6 CE1 A:PHE21 4.2 15.2 1.0 CD1 A:LEU100 4.2 17.6 1.0 C5 A:MZG202 4.3 12.4 0.2 CAC A:HEM201 4.3 19.2 1.0 CD1 A:PHE21 4.3 18.2 1.0 CBC A:HEM201 4.4 20.2 1.0 CG1 A:VAL59 4.4 14.2 1.0 C3 A:MZG202 4.4 16.8 0.6 CG A:LEU100 4.5 16.8 1.0 C4B A:HEM201 4.5 17.1 1.0 CE2 A:PHE24 4.7 16.7 1.0 CZ A:PHE35 4.8 21.3 1.0 CHD A:HEM201 4.8 19.6 1.0 NB A:HEM201 4.9 15.7 1.0 CB A:LEU100 5.0 15.1 1.0 CD2 A:PHE24 5.0 15.3 1.0

Chlorine binding site 2 out of 3 in the Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:11.6 occ:0.20 CL1 A:MZG202 0.0 11.6 0.2 CE1 A:PHE60 0.8 17.0 0.6 CZ A:PHE60 1.2 18.9 0.6 C6 A:MZG202 1.7 11.8 0.2 CD1 A:PHE60 2.2 17.5 0.6 CE2 A:PHE60 2.5 16.7 0.6 C5 A:MZG202 2.7 12.4 0.2 C7 A:MZG202 2.7 12.3 0.2 CG A:PHE60 3.1 14.5 0.6 CD2 A:PHE60 3.3 13.6 0.6 CD1 A:PHE60 3.3 24.4 0.4 CE1 A:PHE60 3.5 27.8 0.4 O A:ALA17 3.8 14.4 1.0 C4 A:MZG202 4.0 13.1 0.2 C2 A:MZG202 4.0 13.2 0.2 CG2 A:ILE20 4.1 13.0 1.0 N A:PHE21 4.1 10.6 1.0 C5 A:MZG202 4.2 16.3 0.6 CG A:PHE60 4.2 18.9 0.4 CB A:PHE21 4.2 11.4 1.0 CE A:MET63 4.3 21.2 1.0 CB A:ILE20 4.4 13.6 1.0 CA A:PHE21 4.4 10.8 1.0 CD1 A:LEU100 4.4 17.6 1.0 CZ A:PHE60 4.5 29.4 0.4 C3 A:MZG202 4.5 13.3 0.2 CG1 A:VAL59 4.5 14.2 1.0 CA A:ALA17 4.5 14.9 1.0 CB A:PHE60 4.6 12.9 0.6 C A:ALA17 4.6 14.4 1.0 CG2 A:THR56 4.6 17.4 0.6 C A:ILE20 4.7 11.1 1.0 C4 A:MZG202 4.7 15.7 0.6 CB A:PHE60 4.8 15.3 0.4 CB A:ALA17 5.0 14.3 1.0

Chlorine binding site 3 out of 3 in the Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dehaloperoxidase B in Complex with Substrate 4-Cl-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:15.6 occ:1.00 CL1 B:MZG202 0.0 15.6 1.0 C6 B:MZG202 1.8 14.1 1.0 C5 B:MZG202 2.7 10.7 1.0 C7 B:MZG202 2.7 14.5 1.0 CD1 B:PHE60 3.7 14.0 1.0 O B:ALA17 3.9 12.5 1.0 C4 B:MZG202 4.0 11.1 1.0 C2 B:MZG202 4.0 13.1 1.0 CG2 B:ILE20 4.1 13.5 1.0 N B:PHE21 4.2 10.1 0.5 N B:PHE21 4.2 10.1 0.5 CB B:PHE21 4.2 10.9 0.5 CE B:MET63 4.3 16.5 1.0 CB B:PHE21 4.3 10.7 0.5 CE1 B:PHE60 4.3 15.7 1.0 CG B:PHE60 4.4 11.5 1.0 CA B:PHE21 4.5 10.4 0.5 CB B:PHE60 4.5 11.5 1.0 CA B:PHE21 4.5 10.4 0.5 CA B:ALA17 4.5 11.7 1.0 C3 B:MZG202 4.5 10.8 1.0 CB B:ILE20 4.5 11.6 1.0 CG2 B:THR56 4.6 12.3 0.2 CG1 B:VAL59 4.6 11.2 1.0 CD1 B:LEU100 4.6 10.4 1.0 C B:ALA17 4.6 11.1 1.0 CB B:ALA17 4.8 11.6 1.0 C B:ILE20 4.9 11.0 1.0 CG B:PHE21 5.0 11.5 0.5 CA B:PHE60 5.0 9.3 1.0

T.Malewschik, V.De Serrano, A.H.Mcguire, R.A.Ghiladi. The Multifunctional Globin Dehaloperoxidase Strikes Again: Simultaneous Peroxidase and Peroxygenase Mechanisms in the Oxidation of Epa Pollutants. Arch.Biochem.Biophys. V. 673 08079 2019.
ISSN: ESSN 1096-0384
PubMed: 31445024
DOI: 10.1016/J.ABB.2019.108079