Iron in PDB 6oo8: Dehaloperoxidase B in Complex with Substrate Pentachlorophenol

The structure of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol, PDB code: 6oo8 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)	37.51 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.690, 67.220, 67.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The structure of Dehaloperoxidase B in Complex with Substrate Pentachlorophenol also contains other interesting chemical elements:

Chlorine

(Cl)

20 atoms

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol (pdb code 6oo8). 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 Pentachlorophenol, PDB code: 6oo8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol


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 Pentachlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:26.5 occ:1.00 FE A:HEM201 0.0 26.5 1.0 ND A:HEM201 1.9 25.6 1.0 NA A:HEM201 2.0 23.5 1.0 NC A:HEM201 2.1 26.7 1.0 NB A:HEM201 2.1 24.2 1.0 CL3 A:PCI202 2.2 30.3 0.1 NE2 A:HIS89 2.2 36.9 1.0 O A:HOH317 2.4 21.9 0.5 CL2 A:PCI202 2.9 94.2 0.4 C1D A:HEM201 2.9 26.6 1.0 C4D A:HEM201 3.0 25.5 1.0 C1A A:HEM201 3.0 24.4 1.0 C4C A:HEM201 3.0 29.4 1.0 C4A A:HEM201 3.0 24.9 1.0 C1B A:HEM201 3.1 24.5 1.0 C4B A:HEM201 3.1 25.4 1.0 C1C A:HEM201 3.1 27.6 1.0 CD2 A:HIS89 3.2 36.8 1.0 CE1 A:HIS89 3.2 37.5 1.0 CHD A:HEM201 3.4 27.8 1.0 CHB A:HEM201 3.4 25.4 1.0 CHA A:HEM201 3.5 21.2 1.0 CHC A:HEM201 3.5 25.4 1.0 C4 A:PCI202 3.7 32.1 0.1 CL3 A:PCI202 4.0 90.7 0.4 CL2 A:PCI202 4.1 32.7 0.1 C2D A:HEM201 4.2 27.6 1.0 C3A A:HEM201 4.2 24.4 1.0 C2A A:HEM201 4.2 24.1 1.0 C3C A:HEM201 4.3 30.0 1.0 C3D A:HEM201 4.3 25.4 1.0 C2C A:HEM201 4.3 28.5 1.0 C3 A:PCI202 4.3 90.8 0.4 C3 A:PCI202 4.3 31.5 0.1 C2B A:HEM201 4.3 24.3 1.0 C3B A:HEM201 4.3 25.0 1.0 ND1 A:HIS89 4.4 34.3 1.0 CG A:HIS89 4.4 35.5 1.0 CG2 A:VAL59 4.4 17.4 1.0 C5 A:PCI202 4.6 32.3 0.1 C4 A:PCI202 4.7 91.3 0.4 CL4 A:PCI202 4.7 35.2 0.1 CG1 A:VAL59 5.0 17.2 1.0

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate Pentachlorophenol


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 Pentachlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1002 b:20.8 occ:1.00 FE B:HEM1002 0.0 20.8 1.0 ND B:HEM1002 1.9 20.5 1.0 NA B:HEM1002 2.0 19.1 1.0 NC B:HEM1002 2.1 21.0 1.0 CL3 B:PCI1003 2.1 33.0 0.1 NB B:HEM1002 2.1 20.6 1.0 NE2 B:HIS89 2.2 25.1 1.0 O B:HOH1152 2.4 13.8 0.4 C1D B:HEM1002 2.9 20.9 1.0 C4C B:HEM1002 3.0 20.9 1.0 C4D B:HEM1002 3.0 21.2 1.0 C4A B:HEM1002 3.0 20.1 1.0 C1A B:HEM1002 3.0 20.6 1.0 C4B B:HEM1002 3.1 20.0 1.0 C1B B:HEM1002 3.1 19.5 1.0 C1C B:HEM1002 3.1 20.7 1.0 CE1 B:HIS89 3.1 25.7 1.0 CD2 B:HIS89 3.2 24.8 1.0 CL4 B:PCI1003 3.2 72.8 0.4 CHD B:HEM1002 3.3 22.6 1.0 CHB B:HEM1002 3.4 19.8 1.0 CHC B:HEM1002 3.5 20.4 1.0 CHA B:HEM1002 3.6 17.9 1.0 C4 B:PCI1003 3.6 34.0 0.1 CL3 B:PCI1003 4.1 75.8 0.4 CL4 B:PCI1003 4.2 35.3 0.1 C2D B:HEM1002 4.2 21.7 1.0 C3A B:HEM1002 4.2 19.4 1.0 C2A B:HEM1002 4.2 20.8 1.0 C3C B:HEM1002 4.3 22.4 1.0 ND1 B:HIS89 4.3 23.9 1.0 C3D B:HEM1002 4.3 21.4 1.0 C2C B:HEM1002 4.3 21.1 1.0 CG B:HIS89 4.3 22.9 1.0 C5 B:PCI1003 4.3 34.3 0.1 C2B B:HEM1002 4.3 19.6 1.0 C3B B:HEM1002 4.3 19.4 1.0 CG2 B:VAL59 4.4 16.9 1.0 C5 B:PCI1003 4.4 75.1 0.4 CL2 B:PCI1003 4.5 34.4 0.1 C3 B:PCI1003 4.5 33.9 0.1 NE2 B:HIS55 4.6 19.6 0.4 C4 B:PCI1003 4.8 76.5 0.4 CE B:MET86 4.8 30.3 1.0 CE1 B:HIS55 4.9 19.1 0.4 CG1 B:VAL59 5.0 15.6 1.0

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