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

Protein crystallography data

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

Other elements in 6onx:

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

Iron (Fe) 2 atoms

Bromine Binding Sites:

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 6onx

Go back to Bromine Binding Sites List in 6onx
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 6onx

Go back to Bromine Binding Sites List in 6onx
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

Reference:

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
Page generated: Sat Dec 12 02:35:24 2020

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