Iron in PDB 8vzr: Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol

The structure of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol, PDB code: 8vzr was solved by M.S.Aktar, V.S.De Serrano, R.A.Ghiladi, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.14 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.404, 67.756, 68.169, 90, 90, 90
R / Rfree (%)	15.6 / 20.4

The structure of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol (pdb code 8vzr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol, PDB code: 8vzr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:22.1 occ:1.00 FE A:HEM201 0.0 22.1 1.0 ND A:HEM201 1.9 21.2 1.0 NA A:HEM201 2.0 23.5 1.0 NE2 A:HIS89 2.1 24.5 1.0 NC A:HEM201 2.1 21.6 1.0 NB A:HEM201 2.1 20.2 1.0 O2 A:OXY206 2.5 15.9 0.6 C1D A:HEM201 2.9 24.1 1.0 C4D A:HEM201 2.9 23.0 1.0 C1A A:HEM201 3.0 24.4 1.0 C4A A:HEM201 3.0 23.7 1.0 CD2 A:HIS89 3.0 26.8 1.0 CE1 A:HIS89 3.1 27.2 1.0 C4B A:HEM201 3.1 18.7 1.0 C4C A:HEM201 3.1 22.1 1.0 C1B A:HEM201 3.1 19.6 1.0 C1C A:HEM201 3.1 20.9 1.0 CHD A:HEM201 3.4 21.4 1.0 CHA A:HEM201 3.4 23.7 1.0 CHC A:HEM201 3.4 19.3 1.0 CHB A:HEM201 3.4 20.2 1.0 BR1 A:MWJ202 3.6 30.2 0.2 O1 A:OXY206 3.6 15.3 0.6 ND1 A:HIS89 4.2 27.3 1.0 C2D A:HEM201 4.2 25.6 1.0 CG A:HIS89 4.2 26.5 1.0 C3D A:HEM201 4.2 26.9 1.0 C2A A:HEM201 4.2 25.6 1.0 C3A A:HEM201 4.2 25.5 1.0 C2B A:HEM201 4.3 18.3 1.0 C3C A:HEM201 4.3 22.3 1.0 C7 A:MWJ202 4.3 26.0 0.2 C3B A:HEM201 4.3 17.8 1.0 C2C A:HEM201 4.3 20.0 1.0 CG2 A:VAL59 4.4 16.9 1.0 C6 A:MWJ202 4.5 26.0 0.2 O1 A:MWJ202 4.7 29.6 0.2 C1 A:MWJ202 4.7 29.9 0.2 CE A:MET86 4.7 35.1 1.0 NE2 A:HIS55 5.0 24.6 0.8 CG1 A:VAL59 5.0 16.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dehaloperoxidase A in Complex with Substrate 4- Bromo-O-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:14.9 occ:1.00 FE B:HEM201 0.0 14.9 1.0 ND B:HEM201 2.0 16.4 1.0 NA B:HEM201 2.0 14.3 1.0 NC B:HEM201 2.1 16.1 1.0 NB B:HEM201 2.1 12.9 1.0 NE2 B:HIS89 2.2 15.6 1.0 O1 B:OXY208 2.3 8.3 0.4 C1D B:HEM201 3.0 17.0 1.0 C4D B:HEM201 3.0 16.8 1.0 C1A B:HEM201 3.0 15.3 1.0 C4A B:HEM201 3.0 14.2 1.0 C4C B:HEM201 3.1 16.6 1.0 C1B B:HEM201 3.1 11.8 1.0 C4B B:HEM201 3.1 12.6 1.0 CE1 B:HIS89 3.1 15.3 1.0 C1C B:HEM201 3.1 15.2 1.0 CD2 B:HIS89 3.2 15.2 1.0 CHD B:HEM201 3.4 17.0 1.0 CHA B:HEM201 3.4 17.1 1.0 CHB B:HEM201 3.4 12.6 1.0 CHC B:HEM201 3.5 14.1 1.0 O2 B:OXY208 3.6 7.6 0.4 C7 B:MWJ202 4.1 21.8 0.4 C2A B:HEM201 4.2 16.1 1.0 ND1 B:HIS89 4.2 15.5 1.0 C3A B:HEM201 4.2 14.9 1.0 C3D B:HEM201 4.3 19.0 1.0 C2D B:HEM201 4.3 19.5 1.0 C3C B:HEM201 4.3 16.0 1.0 CG B:HIS89 4.3 16.2 1.0 C2B B:HEM201 4.3 10.9 1.0 C2C B:HEM201 4.3 15.7 1.0 C3B B:HEM201 4.3 11.8 1.0 CG2 B:VAL59 4.4 14.8 1.0 O1 B:MWJ202 4.5 50.1 0.2 BR1 B:MWJ202 4.7 30.3 0.4 C1 B:MWJ202 4.7 55.2 0.2 CE B:MET86 4.8 18.6 1.0 C6 B:MWJ202 4.8 23.5 0.4 C1 B:MWJ202 4.8 23.9 0.4 C2 B:MWJ202 4.9 22.5 0.4 CE1 B:HIS55 4.9 17.1 0.6

M.S.Aktar, V.De Serrano, R.A.Ghiladi, S.Franzen. Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 38959050
DOI: 10.1021/ACS.BIOCHEM.4C00179