Iron 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:

Chlorine

(Cl)

3 atoms

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

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate 4-Cl-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-Cl-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:18.5 occ:1.00 FE A:HEM201 0.0 18.5 1.0 ND A:HEM201 1.9 16.4 1.0 NA A:HEM201 2.0 18.2 1.0 NC A:HEM201 2.1 17.1 1.0 NB A:HEM201 2.1 15.7 1.0 NE2 A:HIS89 2.2 16.2 1.0 C1D A:HEM201 2.9 19.7 1.0 C4A A:HEM201 3.0 16.8 1.0 C1B A:HEM201 3.1 14.5 1.0 C1A A:HEM201 3.1 18.4 1.0 C4D A:HEM201 3.1 15.9 1.0 C4C A:HEM201 3.1 18.5 1.0 C1C A:HEM201 3.1 16.4 1.0 C4B A:HEM201 3.1 17.1 1.0 CE1 A:HIS89 3.1 18.2 1.0 CD2 A:HIS89 3.2 19.9 1.0 CHB A:HEM201 3.4 17.0 1.0 CHD A:HEM201 3.4 19.6 1.0 CHC A:HEM201 3.5 15.6 1.0 CHA A:HEM201 3.6 14.4 1.0 CG2 A:VAL59 4.1 17.1 1.0 C3A A:HEM201 4.2 15.7 1.0 C2D A:HEM201 4.2 21.9 1.0 C2A A:HEM201 4.2 15.9 1.0 ND1 A:HIS89 4.2 20.0 1.0 C3C A:HEM201 4.3 15.1 1.0 C7 A:MZG202 4.3 18.7 0.6 C2C A:HEM201 4.3 14.9 1.0 CG A:HIS89 4.3 18.1 1.0 C3D A:HEM201 4.3 21.1 1.0 C2B A:HEM201 4.3 16.0 1.0 C3B A:HEM201 4.4 16.0 1.0 C1 A:MZG202 4.8 19.2 0.6 CE A:MET86 4.8 25.2 1.0 C2 A:MZG202 4.9 16.8 0.6 CE1 A:HIS55 4.9 19.5 0.4 CG1 A:VAL59 4.9 14.2 1.0 C6 A:MZG202 5.0 16.4 0.6

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate 4-Cl-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-Cl-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:11.8 occ:1.00 FE B:HEM201 0.0 11.8 1.0 ND B:HEM201 2.0 12.2 1.0 NA B:HEM201 2.0 11.8 1.0 NC B:HEM201 2.0 11.0 1.0 NB B:HEM201 2.1 10.6 1.0 NE2 B:HIS89 2.1 11.1 1.0 O B:HOH327 2.2 18.4 0.3 C4D B:HEM201 3.0 11.5 1.0 C1D B:HEM201 3.0 11.4 1.0 C1B B:HEM201 3.0 10.4 1.0 C1C B:HEM201 3.0 10.3 1.0 C4B B:HEM201 3.1 9.7 1.0 C1A B:HEM201 3.1 11.1 1.0 C4A B:HEM201 3.1 11.5 1.0 C4C B:HEM201 3.1 11.4 1.0 CE1 B:HIS89 3.1 13.8 1.0 CD2 B:HIS89 3.1 12.9 1.0 CHA B:HEM201 3.4 13.2 1.0 CHB B:HEM201 3.4 10.3 1.0 CHC B:HEM201 3.4 10.8 1.0 CHD B:HEM201 3.4 11.0 1.0 ND1 B:HIS89 4.2 12.8 1.0 CG B:HIS89 4.3 12.3 1.0 C2D B:HEM201 4.3 14.9 1.0 C3A B:HEM201 4.3 11.4 1.0 C3C B:HEM201 4.3 12.0 1.0 C2A B:HEM201 4.3 12.0 1.0 C3D B:HEM201 4.3 12.0 1.0 C2B B:HEM201 4.3 10.2 1.0 C2C B:HEM201 4.3 12.4 1.0 C3B B:HEM201 4.3 10.3 1.0 CG2 B:VAL59 4.4 11.4 1.0 CG1 B:VAL59 4.7 11.2 1.0 CE B:MET86 4.7 16.4 1.0 O1 B:MZG202 4.9 14.1 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