Iron in PDB 8doi: Dehaloperoxidase B in Complex with 2,2'-Biphenol

The structure of Dehaloperoxidase B in Complex with 2,2'-Biphenol, PDB code: 8doi 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)	37.32 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.239, 67.702, 68.038, 90, 90, 90
R / Rfree (%)	17.4 / 22.9

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

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with 2,2'-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 2,2'-Biphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.2 occ:1.00 FE A:HEM201 0.0 23.2 1.0 ND A:HEM201 1.9 23.8 1.0 NA A:HEM201 2.0 21.5 1.0 NC A:HEM201 2.1 21.9 1.0 NB A:HEM201 2.1 20.5 1.0 NE2 A:HIS89 2.2 26.3 1.0 C1D A:HEM201 2.9 23.6 1.0 C4D A:HEM201 2.9 24.8 1.0 C1A A:HEM201 3.0 22.2 1.0 C4C A:HEM201 3.0 23.7 1.0 C1B A:HEM201 3.0 20.3 1.0 C4A A:HEM201 3.0 20.4 1.0 C4B A:HEM201 3.1 21.1 1.0 O14 A:5VL202 3.1 71.0 0.8 CD2 A:HIS89 3.1 26.6 1.0 C1C A:HEM201 3.1 21.9 1.0 CE1 A:HIS89 3.2 25.6 1.0 O A:HOH301 3.3 7.3 0.2 CHA A:HEM201 3.4 25.4 1.0 CHD A:HEM201 3.4 23.3 1.0 CHB A:HEM201 3.4 19.4 1.0 CHC A:HEM201 3.5 21.7 1.0 C13 A:5VL202 4.0 76.7 0.8 C2D A:HEM201 4.2 25.3 1.0 C3D A:HEM201 4.2 27.6 1.0 C2A A:HEM201 4.2 21.8 1.0 C3A A:HEM201 4.2 21.2 1.0 ND1 A:HIS89 4.2 25.5 1.0 CG A:HIS89 4.2 26.4 1.0 C3C A:HEM201 4.3 22.1 1.0 C2B A:HEM201 4.3 18.6 1.0 C2C A:HEM201 4.3 22.9 1.0 C3B A:HEM201 4.3 18.5 1.0 CG2 A:VAL59 4.4 16.2 1.0 C12 A:5VL202 4.5 83.5 0.8 C6 A:5VL202 4.5 67.3 0.8 CG1 A:VAL59 4.8 15.1 1.0 CE A:MET86 5.0 26.8 1.0

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with 2,2'-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 2,2'-Biphenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:23.3 occ:1.00 FE B:HEM202 0.0 23.3 1.0 ND B:HEM202 1.9 23.2 1.0 NA B:HEM202 2.0 21.0 1.0 NC B:HEM202 2.1 22.8 1.0 NB B:HEM202 2.1 21.2 1.0 NE2 B:HIS89 2.1 24.3 1.0 O B:HOH301 2.4 3.5 0.2 O14 B:5VL203 2.8 72.3 0.8 C4D B:HEM202 2.9 24.9 1.0 C1D B:HEM202 2.9 24.6 1.0 C1A B:HEM202 3.0 24.7 1.0 C4A B:HEM202 3.0 22.2 1.0 C1B B:HEM202 3.0 20.9 1.0 C4C B:HEM202 3.1 25.5 1.0 CE1 B:HIS89 3.1 25.3 1.0 C4B B:HEM202 3.1 20.8 1.0 C1C B:HEM202 3.1 22.9 1.0 CD2 B:HIS89 3.2 24.7 1.0 CHD B:HEM202 3.4 25.9 1.0 CHA B:HEM202 3.4 25.7 1.0 CHB B:HEM202 3.4 21.7 1.0 CHC B:HEM202 3.5 22.4 1.0 C13 B:5VL203 3.7 71.0 0.8 C12 B:5VL203 4.1 77.9 0.8 C3D B:HEM202 4.2 28.6 1.0 C2D B:HEM202 4.2 26.8 1.0 C3A B:HEM202 4.2 24.1 1.0 C2A B:HEM202 4.2 25.3 1.0 ND1 B:HIS89 4.2 24.4 1.0 CG2 B:VAL59 4.3 17.5 1.0 CG B:HIS89 4.3 25.2 1.0 C2B B:HEM202 4.3 20.4 1.0 C3C B:HEM202 4.3 24.3 1.0 C2C B:HEM202 4.3 23.2 1.0 C6 B:5VL203 4.3 76.4 0.8 C3B B:HEM202 4.4 21.5 1.0 CG1 B:VAL59 4.7 18.1 1.0 C8 B:5VL203 4.7 76.8 0.8 C7 B:5VL203 5.0 77.1 0.8

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