Iron in PDB 6oo6: Dehaloperoxidase B in Complex with Substrate P-Cresol

The structure of Dehaloperoxidase B in Complex with Substrate P-Cresol, PDB code: 6oo6 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)	45.09 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.505, 67.540, 67.625, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 22.4

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with Substrate P-Cresol (pdb code 6oo6). 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 P-Cresol, PDB code: 6oo6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-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 P-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:14.1 occ:1.00 FE A:HEM201 0.0 14.1 1.0 ND A:HEM201 1.9 15.6 1.0 NA A:HEM201 2.0 14.6 1.0 NC A:HEM201 2.1 15.3 1.0 NB A:HEM201 2.1 14.6 1.0 NE2 A:HIS89 2.2 18.5 1.0 C1D A:HEM201 2.9 16.0 1.0 C4D A:HEM201 3.0 16.2 1.0 C1A A:HEM201 3.0 16.0 1.0 C4C A:HEM201 3.0 16.3 1.0 C4A A:HEM201 3.1 14.9 1.0 C1B A:HEM201 3.1 14.0 1.0 C4B A:HEM201 3.1 14.4 1.0 C1C A:HEM201 3.1 15.5 1.0 CD2 A:HIS89 3.2 18.1 1.0 CE1 A:HIS89 3.2 18.6 1.0 CHD A:HEM201 3.4 16.2 1.0 CHA A:HEM201 3.4 15.9 1.0 CHB A:HEM201 3.4 14.6 1.0 CHC A:HEM201 3.5 15.1 1.0 CD2 A:PCR202 4.1 25.4 1.0 C2D A:HEM201 4.2 17.4 1.0 C3D A:HEM201 4.2 17.6 1.0 C2A A:HEM201 4.2 16.2 1.0 C3A A:HEM201 4.2 15.2 1.0 C3C A:HEM201 4.3 16.0 1.0 C2C A:HEM201 4.3 15.6 1.0 ND1 A:HIS89 4.3 18.3 1.0 C2B A:HEM201 4.3 14.2 1.0 CG A:HIS89 4.3 18.4 1.0 CG2 A:VAL59 4.4 11.7 1.0 C3B A:HEM201 4.4 14.4 1.0 CB A:PCR202 4.5 24.7 1.0 CG A:PCR202 4.7 24.5 1.0 CG1 A:VAL59 4.7 11.8 1.0 CE A:MET86 4.8 21.6 1.0 CE2 A:PCR202 4.9 25.1 1.0

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-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 P-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:16.4 occ:1.00 FE B:HEM201 0.0 16.4 1.0 ND B:HEM201 1.9 15.4 1.0 NA B:HEM201 2.0 15.2 1.0 NC B:HEM201 2.1 15.7 1.0 NB B:HEM201 2.1 15.4 1.0 NE2 B:HIS89 2.2 19.8 1.0 C1D B:HEM201 2.9 15.5 1.0 C4D B:HEM201 3.0 16.2 1.0 C1A B:HEM201 3.0 15.8 1.0 C4C B:HEM201 3.1 15.9 1.0 C4A B:HEM201 3.1 16.0 1.0 C4B B:HEM201 3.1 15.4 1.0 C1B B:HEM201 3.1 15.0 1.0 C1C B:HEM201 3.1 15.6 1.0 CE1 B:HIS89 3.2 19.5 1.0 CD2 B:HIS89 3.2 19.1 1.0 CHD B:HEM201 3.4 15.5 1.0 CHA B:HEM201 3.5 15.2 1.0 CHB B:HEM201 3.5 15.4 1.0 CHC B:HEM201 3.5 15.5 1.0 CD1 B:PCR202 3.9 27.4 0.8 C2D B:HEM201 4.2 15.6 1.0 C2A B:HEM201 4.2 15.9 1.0 C3D B:HEM201 4.2 17.4 1.0 C3A B:HEM201 4.2 15.9 1.0 C3C B:HEM201 4.3 15.6 1.0 ND1 B:HIS89 4.3 18.6 1.0 C2C B:HEM201 4.3 15.4 1.0 C2B B:HEM201 4.3 15.1 1.0 CG B:HIS89 4.3 18.4 1.0 C3B B:HEM201 4.3 15.1 1.0 CG2 B:VAL59 4.4 11.9 1.0 CB B:PCR202 4.4 28.0 0.8 CG B:PCR202 4.5 27.9 0.8 CG1 B:VAL59 4.7 11.8 1.0 CE1 B:PCR202 4.7 28.9 0.8 CE B:MET86 4.8 17.8 0.6

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