Iron in PDB 6ong: Dehaloperoxidate B in Complex with Substrate 4-F-Cresol

The structure of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol, PDB code: 6ong was solved by R.A.Ghiladi, V.S.De Serrano, T.Malewschik, A.Mcguire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.55 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.084, 67.237, 67.825, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.4

The structure of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Iron atom in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol (pdb code 6ong). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol, PDB code: 6ong:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:10.1 occ:1.00 FE A:HEM201 0.0 10.1 1.0 ND A:HEM201 1.9 9.5 1.0 NA A:HEM201 2.0 8.8 1.0 NC A:HEM201 2.1 9.6 1.0 NB A:HEM201 2.1 8.6 1.0 NE2 A:HIS89 2.2 11.0 1.0 C1D A:HEM201 3.0 10.2 1.0 C1A A:HEM201 3.0 10.2 1.0 C4A A:HEM201 3.1 9.6 1.0 C4C A:HEM201 3.1 10.7 1.0 C4D A:HEM201 3.1 9.2 1.0 C1C A:HEM201 3.1 10.1 1.0 C1B A:HEM201 3.1 8.8 1.0 CE1 A:HIS89 3.1 13.3 1.0 C4B A:HEM201 3.1 9.4 1.0 CD2 A:HIS89 3.1 12.4 1.0 CHD A:HEM201 3.4 10.9 1.0 CHB A:HEM201 3.5 8.7 1.0 CHC A:HEM201 3.5 8.4 1.0 CHA A:HEM201 3.5 7.1 1.0 C7 A:MWM202 4.1 9.5 0.8 CG2 A:VAL59 4.2 7.4 1.0 ND1 A:HIS89 4.2 12.7 1.0 C2A A:HEM201 4.2 10.6 1.0 C3A A:HEM201 4.2 10.1 1.0 C3C A:HEM201 4.3 10.8 1.0 CG A:HIS89 4.3 12.2 1.0 C2C A:HEM201 4.3 9.6 1.0 C2D A:HEM201 4.3 10.9 1.0 C2B A:HEM201 4.3 9.0 1.0 C3D A:HEM201 4.3 10.8 1.0 C3B A:HEM201 4.4 9.5 1.0 CE A:MET86 4.7 16.5 1.0 C1 A:MWM202 4.7 9.2 0.8 NE2 A:HIS55 4.8 10.0 0.2 C2 A:MWM202 4.8 8.4 0.8 F1 A:MWM202 4.8 11.2 0.8 CG1 A:VAL59 4.8 7.6 1.0 C6 A:MWM202 4.8 9.1 0.8 CD1 A:LEU92 5.0 18.4 1.0

Iron binding site 2 out of 2 in the Dehaloperoxidate B in Complex with Substrate 4-F-Cresol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dehaloperoxidate B in Complex with Substrate 4-F-Cresol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:8.2 occ:1.00 FE B:HEM402 0.0 8.2 1.0 ND B:HEM402 2.0 9.0 1.0 NA B:HEM402 2.0 7.0 1.0 NC B:HEM402 2.1 7.7 1.0 NB B:HEM402 2.1 7.3 1.0 NE2 B:HIS89 2.2 7.9 1.0 C1D B:HEM402 3.0 8.6 1.0 C4D B:HEM402 3.0 8.1 1.0 C4C B:HEM402 3.1 8.2 1.0 C4B B:HEM402 3.1 7.0 1.0 C1A B:HEM402 3.1 8.5 1.0 C1B B:HEM402 3.1 7.0 1.0 C4A B:HEM402 3.1 7.7 1.0 C1C B:HEM402 3.1 7.3 1.0 CD2 B:HIS89 3.1 8.4 1.0 CE1 B:HIS89 3.1 7.9 1.0 CHD B:HEM402 3.4 8.5 1.0 CHB B:HEM402 3.5 7.3 1.0 CHC B:HEM402 3.5 7.1 1.0 CHA B:HEM402 3.5 6.7 1.0 C7 B:MWM404 4.0 7.7 0.6 ND1 B:HIS89 4.3 8.5 1.0 C2D B:HEM402 4.3 9.2 1.0 C2C B:HEM402 4.3 7.8 1.0 C3A B:HEM402 4.3 7.5 1.0 C2A B:HEM402 4.3 8.5 1.0 C3D B:HEM402 4.3 9.5 1.0 C3C B:HEM402 4.3 8.4 1.0 CG B:HIS89 4.3 8.6 1.0 C2B B:HEM402 4.3 7.2 1.0 CG2 B:VAL59 4.3 6.5 1.0 C3B B:HEM402 4.3 7.0 1.0 F1 B:MWM404 4.7 9.4 0.6 CE B:MET86 4.7 9.0 0.7 C1 B:MWM404 4.7 8.0 0.6 C6 B:MWM404 4.7 8.2 0.6 C2 B:MWM404 4.7 8.3 0.6 CG1 B:VAL59 4.8 5.6 1.0 O1 B:MWM404 5.0 4.8 0.2

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