Iron 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:

Bromine (Br) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Dehaloperoxidase B in Complex with Substrate 4-Br-Cresol, PDB code: 6onx:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6onx

Go back to Iron Binding Sites List in 6onx
Iron 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 Iron with other atoms in the Fe 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:Fe201

b:18.8
occ:1.00
FE A:HEM201 0.0 18.8 1.0
ND A:HEM201 2.0 19.2 1.0
NA A:HEM201 2.0 19.6 1.0
NC A:HEM201 2.1 18.6 1.0
NB A:HEM201 2.1 16.6 1.0
NE2 A:HIS89 2.1 22.2 1.0
C1D A:HEM201 3.0 19.6 1.0
C4C A:HEM201 3.0 20.0 1.0
C4B A:HEM201 3.0 17.4 1.0
C4D A:HEM201 3.0 19.8 1.0
C1A A:HEM201 3.0 20.6 1.0
C4A A:HEM201 3.1 17.5 1.0
C1C A:HEM201 3.1 17.3 1.0
C1B A:HEM201 3.1 17.2 1.0
CE1 A:HIS89 3.1 22.2 1.0
CD2 A:HIS89 3.1 25.8 1.0
CHD A:HEM201 3.4 21.1 1.0
CHC A:HEM201 3.4 16.6 1.0
CHB A:HEM201 3.5 15.7 1.0
CHA A:HEM201 3.5 18.5 1.0
ND1 A:HIS89 4.2 21.6 1.0
C3C A:HEM201 4.2 18.8 1.0
C2D A:HEM201 4.2 19.9 1.0
CG2 A:VAL59 4.3 13.6 1.0
C3A A:HEM201 4.3 19.0 1.0
C2A A:HEM201 4.3 19.9 1.0
CG A:HIS89 4.3 23.5 1.0
C2C A:HEM201 4.3 18.1 1.0
C3D A:HEM201 4.3 22.1 1.0
C3B A:HEM201 4.3 17.2 1.0
C2B A:HEM201 4.3 17.9 1.0
CE A:MET86 4.7 33.3 1.0
O1 A:MWJ202 4.8 20.2 0.7
CG1 A:VAL59 4.8 13.8 1.0

Iron binding site 2 out of 2 in 6onx

Go back to Iron Binding Sites List in 6onx
Iron 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 Iron with other atoms in the Fe 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:Fe702

b:17.5
occ:1.00
FE B:HEM702 0.0 17.5 1.0
ND B:HEM702 2.0 17.0 1.0
NA B:HEM702 2.0 18.1 1.0
NB B:HEM702 2.1 17.2 1.0
NC B:HEM702 2.1 15.9 1.0
NE2 B:HIS89 2.1 19.7 1.0
C1D B:HEM702 3.0 16.4 1.0
C4D B:HEM702 3.0 17.5 1.0
C4B B:HEM702 3.0 14.2 1.0
C1B B:HEM702 3.0 16.0 1.0
C1A B:HEM702 3.0 17.4 1.0
C4C B:HEM702 3.1 15.2 1.0
C4A B:HEM702 3.1 16.9 1.0
C1C B:HEM702 3.1 14.1 1.0
CE1 B:HIS89 3.1 22.4 1.0
CD2 B:HIS89 3.2 22.0 1.0
CHD B:HEM702 3.4 17.4 1.0
CHA B:HEM702 3.4 15.5 1.0
CHB B:HEM702 3.4 18.2 1.0
CHC B:HEM702 3.5 15.5 1.0
C2B B:HEM702 4.2 14.2 1.0
C2D B:HEM702 4.2 19.4 1.0
ND1 B:HIS89 4.3 22.5 1.0
C2A B:HEM702 4.3 17.6 1.0
C3D B:HEM702 4.3 19.9 1.0
C3A B:HEM702 4.3 17.7 1.0
C3B B:HEM702 4.3 14.3 1.0
C3C B:HEM702 4.3 15.8 1.0
CG B:HIS89 4.3 20.3 1.0
C2C B:HEM702 4.3 14.4 1.0
CG2 B:VAL59 4.4 15.3 1.0
CG1 B:VAL59 4.8 13.9 1.0
O1 B:MWJ703 4.9 18.0 0.8
CE B:MET86 4.9 25.9 1.0

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: Sun Dec 13 16:47:51 2020

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