Iron in PDB 5chq: Dehaloperoxidase B in Complex with Substrate P-Nitrophenol

The structure of Dehaloperoxidase B in Complex with Substrate P-Nitrophenol, PDB code: 5chq was solved by L.Carey, R.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.78 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.770, 67.619, 67.196, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 23.4

The binding sites of Iron atom in the Dehaloperoxidase B in Complex with Substrate P-Nitrophenol (pdb code 5chq). 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 P-Nitrophenol, PDB code: 5chq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-Nitrophenol


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 P-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:9.4 occ:1.00 FE A:HEM201 0.0 9.4 1.0 NA A:HEM201 2.0 6.4 1.0 NC A:HEM201 2.0 9.5 1.0 ND A:HEM201 2.1 10.6 1.0 NB A:HEM201 2.1 7.7 1.0 NE2 A:HIS89 2.3 9.3 1.0 C1A A:HEM201 3.0 9.8 1.0 C4D A:HEM201 3.1 12.4 1.0 C4C A:HEM201 3.1 13.4 1.0 C1D A:HEM201 3.1 10.2 1.0 C1C A:HEM201 3.1 9.3 1.0 C4A A:HEM201 3.1 9.2 1.0 C4B A:HEM201 3.1 9.7 1.0 C1B A:HEM201 3.1 4.9 1.0 CD2 A:HIS89 3.2 15.0 1.0 CE1 A:HIS89 3.3 7.9 1.0 CHA A:HEM201 3.4 11.1 1.0 H6 A:NPO204 3.4 20.1 1.0 CHD A:HEM201 3.4 7.7 1.0 CHC A:HEM201 3.4 7.6 1.0 CHB A:HEM201 3.5 4.7 1.0 C6 A:NPO204 4.1 16.7 1.0 C2A A:HEM201 4.2 7.4 1.0 CG2 A:VAL59 4.3 9.2 1.0 C3A A:HEM201 4.3 4.2 1.0 C3C A:HEM201 4.3 8.5 1.0 C2C A:HEM201 4.3 7.7 1.0 C2D A:HEM201 4.3 11.2 1.0 C3D A:HEM201 4.3 11.4 1.0 C3B A:HEM201 4.3 7.3 1.0 C2B A:HEM201 4.4 5.9 1.0 CG A:HIS89 4.4 7.9 1.0 ND1 A:HIS89 4.4 13.2 1.0 H5 A:NPO204 4.4 19.4 1.0 O3 A:NPO204 4.5 23.9 1.0 C5 A:NPO204 4.6 16.2 1.0 CE A:MET86 4.7 15.7 1.0 C1 A:NPO204 4.9 15.8 1.0

Iron binding site 2 out of 2 in the Dehaloperoxidase B in Complex with Substrate P-Nitrophenol


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 P-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:8.9 occ:1.00 FE B:HEM201 0.0 8.9 1.0 NC B:HEM201 2.0 6.6 1.0 NA B:HEM201 2.0 9.5 1.0 NB B:HEM201 2.1 7.0 1.0 ND B:HEM201 2.1 13.0 1.0 NE2 B:HIS89 2.3 11.7 1.0 C4C B:HEM201 3.0 13.3 1.0 C1A B:HEM201 3.1 11.5 1.0 C1C B:HEM201 3.1 9.8 1.0 C4A B:HEM201 3.1 8.2 1.0 C1D B:HEM201 3.1 10.6 1.0 C4B B:HEM201 3.1 9.1 1.0 C4D B:HEM201 3.1 13.9 1.0 CD2 B:HIS89 3.1 11.3 1.0 C1B B:HEM201 3.1 4.4 1.0 CE1 B:HIS89 3.3 15.8 1.0 CHD B:HEM201 3.4 11.6 1.0 CHA B:HEM201 3.4 9.4 1.0 CHB B:HEM201 3.5 6.8 1.0 H6 B:NPO204 3.5 12.4 1.0 CHC B:HEM201 3.5 6.4 1.0 C6 B:NPO204 4.2 10.4 1.0 CG2 B:VAL59 4.2 7.6 1.0 C3C B:HEM201 4.3 10.0 1.0 CG B:HIS89 4.3 17.8 1.0 C2C B:HEM201 4.3 6.5 1.0 C2A B:HEM201 4.3 13.8 1.0 C3A B:HEM201 4.3 9.3 1.0 ND1 B:HIS89 4.3 13.7 1.0 C2D B:HEM201 4.3 8.8 1.0 C3B B:HEM201 4.3 6.3 1.0 C3D B:HEM201 4.3 15.5 1.0 C2B B:HEM201 4.3 8.4 1.0 H5 B:NPO204 4.5 15.4 1.0 CE B:MET86 4.6 13.7 1.0 O3 B:NPO204 4.7 17.6 1.0 C5 B:NPO204 4.8 12.9 1.0 CG1 B:VAL59 4.8 7.1 1.0

N.L.Mccombs, J.D'antonio, D.A.Barrios, L.M.Carey, R.A.Ghiladi. Nonmicrobial Nitrophenol Degradation Via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin From Amphitrite Ornata. Biochemistry V. 55 2465 2016.
ISSN: ISSN 0006-2960
PubMed: 27070125
DOI: 10.1021/ACS.BIOCHEM.6B00143