Iron in PDB 8doj: Dehaloperoxidase B in Complex with 3,3'-Biphenol

The structure of Dehaloperoxidase B in Complex with 3,3'-Biphenol, PDB code: 8doj was solved by V.S.De Serrano, D.Yun, R.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.85 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.595, 67.374, 67.647, 90, 90, 90
R / Rfree (%)	14.6 / 18.9

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with 3,3'-Biphenol (pdb code 8doj). 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 3,3'-Biphenol, PDB code: 8doj:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with 3,3'-Biphenol


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 3,3'-Biphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:15.7 occ:1.00 FE A:HEM201 0.0 15.7 1.0 ND A:HEM201 2.0 15.3 1.0 NA A:HEM201 2.0 15.4 1.0 NC A:HEM201 2.0 13.9 1.0 NB A:HEM201 2.1 15.1 1.0 NE2 A:HIS89 2.1 16.6 1.0 C1D A:HEM201 3.0 17.0 1.0 C4D A:HEM201 3.0 16.4 1.0 C4A A:HEM201 3.0 15.5 1.0 C4C A:HEM201 3.0 16.1 1.0 C1A A:HEM201 3.0 15.4 1.0 C1B A:HEM201 3.0 13.0 1.0 C1C A:HEM201 3.1 15.4 1.0 C4B A:HEM201 3.1 12.8 1.0 CE1 A:HIS89 3.1 15.7 1.0 CD2 A:HIS89 3.1 15.8 1.0 CHB A:HEM201 3.4 13.3 1.0 CHC A:HEM201 3.4 13.2 1.0 CHA A:HEM201 3.5 15.0 1.0 CHD A:HEM201 3.5 14.8 1.0 C4 A:T1I202 3.7 15.7 0.8 C5 A:T1I202 3.8 19.5 0.8 ND1 A:HIS89 4.2 15.1 1.0 C2A A:HEM201 4.3 14.1 1.0 C3A A:HEM201 4.3 13.6 1.0 C3C A:HEM201 4.3 16.1 1.0 C2C A:HEM201 4.3 16.5 1.0 C3D A:HEM201 4.3 17.6 1.0 CG A:HIS89 4.3 14.9 1.0 C2D A:HEM201 4.3 18.1 1.0 C2B A:HEM201 4.3 12.7 1.0 C3B A:HEM201 4.3 14.2 1.0 CG2 A:VAL59 4.4 14.3 1.0 CE A:MET86 4.8 21.8 1.0 CG1 A:VAL59 4.8 12.2 1.0 C6 A:T1I202 4.9 23.0 0.8 C3 A:T1I202 5.0 20.5 0.8

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with 3,3'-Biphenol


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 3,3'-Biphenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:17.3 occ:1.00 FE B:HEM201 0.0 17.3 1.0 ND B:HEM201 1.9 17.6 1.0 NA B:HEM201 2.0 16.7 1.0 NB B:HEM201 2.0 14.7 1.0 NC B:HEM201 2.1 19.6 1.0 NE2 B:HIS89 2.1 16.2 1.0 O B:HOH319 2.8 37.6 0.3 C1D B:HEM201 3.0 17.8 1.0 C4A B:HEM201 3.0 16.9 1.0 C1B B:HEM201 3.0 14.7 1.0 C4C B:HEM201 3.0 18.3 1.0 C4B B:HEM201 3.1 14.7 1.0 C1C B:HEM201 3.1 17.5 1.0 C4D B:HEM201 3.1 18.3 1.0 CD2 B:HIS89 3.1 16.3 1.0 C1A B:HEM201 3.1 17.2 1.0 CE1 B:HIS89 3.1 15.8 1.0 CHB B:HEM201 3.4 16.1 1.0 CHD B:HEM201 3.4 20.1 1.0 CHC B:HEM201 3.5 17.1 1.0 CHA B:HEM201 3.7 12.9 1.0 ND1 B:HIS89 4.2 16.7 1.0 C2D B:HEM201 4.3 20.0 1.0 CG B:HIS89 4.3 18.7 1.0 C2C B:HEM201 4.3 18.2 1.0 C2A B:HEM201 4.3 18.1 1.0 C3C B:HEM201 4.3 21.7 1.0 C3A B:HEM201 4.3 15.5 1.0 C2B B:HEM201 4.3 15.0 1.0 C3D B:HEM201 4.3 20.4 1.0 CG2 B:VAL59 4.3 15.4 1.0 C3B B:HEM201 4.3 14.9 1.0 CG1 B:VAL59 4.8 14.0 1.0 CE B:MET86 4.8 23.5 1.0 NE2 B:HIS55 5.0 29.0 0.3

D.Yun, V.De Serrano, R.A.Ghiladi. Oxidation of Bisphenol A (Bpa) and Related Compounds By the Multifunctional Catalytic Globin Dehaloperoxidase. J.Inorg.Biochem. V. 238 12020 2023.
ISSN: ISSN 0162-0134
PubMed: 36272837
DOI: 10.1016/J.JINORGBIO.2022.112020