Bromine in PDB 6onx: Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol

The structure of Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol, PDB code: 6onx 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)	44.47 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.043, 67.614, 67.566, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.6

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

Iron

(Fe)

2 atoms

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

Bromine binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:20.3 occ:0.71 BR1 A:MWJ202 0.0 20.3 0.7 C6 A:MWJ202 1.9 17.3 0.7 CD1 A:PHE60 2.7 22.3 0.3 C7 A:MWJ202 2.8 15.3 0.7 C5 A:MWJ202 2.9 17.7 0.7 CE1 A:PHE60 3.0 22.2 0.3 O A:ALA17 3.8 13.8 1.0 CD1 A:PHE60 3.8 15.4 0.7 CG A:PHE60 3.9 20.8 0.3 C2 A:MWJ202 4.1 15.0 0.7 N A:PHE21 4.1 10.5 1.0 C4 A:MWJ202 4.1 15.8 0.7 CG2 A:ILE20 4.2 12.8 1.0 CB A:PHE21 4.2 11.7 1.0 CB A:PHE60 4.4 18.2 0.3 CA A:PHE21 4.4 11.5 1.0 CE A:MET63 4.4 26.1 1.0 CZ A:PHE60 4.4 23.5 0.3 CE1 A:PHE60 4.4 16.6 0.7 CB A:ILE20 4.5 11.2 1.0 CD1 A:LEU100 4.5 14.9 1.0 CA A:ALA17 4.5 14.4 1.0 CG A:PHE60 4.5 15.5 0.7 OG1 A:THR56 4.5 15.3 0.1 CG1 A:VAL59 4.6 13.8 1.0 C A:ALA17 4.6 14.2 1.0 CB A:PHE60 4.6 13.3 0.7 C3 A:MWJ202 4.6 16.5 0.7 C A:ILE20 4.8 11.6 1.0 CA A:PHE60 4.8 16.5 0.3 CG A:PHE21 5.0 15.5 1.0 CD1 A:PHE21 5.0 17.4 1.0

Bromine binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Br703 b:15.8 occ:0.70 BR1 B:MWJ703 0.0 15.8 0.7 CE2 B:PHE60 1.5 13.4 0.2 CD2 B:PHE60 1.9 13.2 0.2 C6 B:MWJ703 1.9 15.4 0.8 C7 B:MWJ703 2.8 15.1 0.8 CZ B:PHE60 2.8 13.4 0.2 C5 B:MWJ703 2.9 14.7 0.8 CG B:PHE60 3.2 13.5 0.2 CD1 B:PHE60 3.7 16.2 0.8 CE1 B:PHE60 3.9 13.7 0.2 O B:ALA17 3.9 14.8 1.0 CD1 B:PHE60 4.0 13.7 0.2 C2 B:MWJ703 4.2 15.5 0.8 C4 B:MWJ703 4.2 17.5 0.8 CB B:PHE21 4.3 11.6 1.0 N B:PHE21 4.3 10.6 1.0 CB B:PHE60 4.3 13.8 0.2 CG2 B:ILE20 4.3 12.9 1.0 CG B:PHE60 4.3 14.2 0.8 CB B:PHE60 4.4 14.7 0.8 CG2 B:THR56 4.4 12.8 0.1 CE1 B:PHE60 4.4 15.6 0.8 CE B:MET63 4.5 20.4 1.0 CA B:ALA17 4.5 12.1 1.0 CG1 B:VAL59 4.5 13.9 1.0 CA B:PHE21 4.5 11.2 1.0 CD1 B:LEU100 4.5 14.4 1.0 CB B:ILE20 4.5 12.7 1.0 C B:ALA17 4.6 13.1 1.0 C3 B:MWJ703 4.7 15.4 0.8 CA B:PHE60 4.8 13.6 0.8 CB B:ALA17 4.8 12.9 1.0 CA B:PHE60 4.9 13.7 0.2 C B:ILE20 4.9 11.8 1.0 O B:THR56 4.9 13.9 1.0 N B:PHE60 5.0 13.6 0.2

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