Iron in PDB 5chr: Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol

The structure of Dehaloperoxidase B in Complex with Substrate P-Nitrocatechol, PDB code: 5chr 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)	47.60 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.883, 67.192, 67.442, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 22

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

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


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-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:14.4 occ:1.00 FE A:HEM201 0.0 14.4 1.0 NA A:HEM201 2.0 11.1 1.0 NC A:HEM201 2.0 10.6 1.0 ND A:HEM201 2.1 13.5 1.0 NB A:HEM201 2.1 11.5 1.0 NE2 A:HIS89 2.3 14.1 1.0 O1 A:OXY205 2.5 14.7 0.5 C1A A:HEM201 3.0 16.4 1.0 C1C A:HEM201 3.0 16.0 1.0 C4C A:HEM201 3.1 11.5 1.0 C4A A:HEM201 3.1 11.6 1.0 C4D A:HEM201 3.1 20.7 1.0 C1D A:HEM201 3.1 14.3 1.0 C4B A:HEM201 3.1 14.1 1.0 C1B A:HEM201 3.1 13.7 1.0 CD2 A:HIS89 3.2 15.6 1.0 CE1 A:HIS89 3.3 16.6 1.0 CHA A:HEM201 3.4 16.3 1.0 CHC A:HEM201 3.4 14.4 1.0 CHD A:HEM201 3.4 12.3 1.0 CHB A:HEM201 3.5 11.4 1.0 O2 A:OXY205 3.7 19.8 0.5 C5 A:4NC204 4.1 17.0 0.5 C2A A:HEM201 4.2 14.9 1.0 C2C A:HEM201 4.3 13.9 1.0 C3A A:HEM201 4.3 11.9 1.0 C3C A:HEM201 4.3 12.2 1.0 C3D A:HEM201 4.3 15.8 1.0 C2D A:HEM201 4.3 11.6 1.0 C3B A:HEM201 4.4 14.3 1.0 O10 A:4NC204 4.4 16.0 0.5 C2B A:HEM201 4.4 10.6 1.0 CG2 A:VAL59 4.4 12.4 1.0 CG A:HIS89 4.4 16.3 1.0 ND1 A:HIS89 4.4 14.2 1.0 CE A:MET86 4.7 17.7 1.0 C6 A:4NC204 4.7 16.5 0.5 CG1 A:VAL59 4.9 15.2 1.0 NE2 A:HIS55 4.9 18.5 0.4 C4 A:4NC204 5.0 12.6 0.5

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


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-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:14.6 occ:1.00 FE B:HEM201 0.0 14.6 1.0 NA B:HEM201 2.0 12.5 1.0 NC B:HEM201 2.0 11.2 1.0 NB B:HEM201 2.1 12.3 1.0 ND B:HEM201 2.1 16.3 1.0 NE2 B:HIS89 2.3 13.3 1.0 C1A B:HEM201 3.0 13.7 1.0 C4C B:HEM201 3.1 19.9 1.0 C1C B:HEM201 3.1 17.5 1.0 C4A B:HEM201 3.1 15.4 1.0 C4D B:HEM201 3.1 18.5 1.0 C1B B:HEM201 3.1 14.7 1.0 C4B B:HEM201 3.1 14.5 1.0 C1D B:HEM201 3.1 16.7 1.0 CD2 B:HIS89 3.2 14.8 1.0 CE1 B:HIS89 3.2 15.4 1.0 CHA B:HEM201 3.4 13.8 1.0 CHB B:HEM201 3.4 9.8 1.0 CHD B:HEM201 3.5 16.3 1.0 CHC B:HEM201 3.5 14.9 1.0 CG2 B:VAL59 4.1 13.1 1.0 C5 B:4NC202 4.2 20.9 1.0 C2A B:HEM201 4.3 15.6 1.0 C3C B:HEM201 4.3 21.2 1.0 C2C B:HEM201 4.3 14.2 1.0 C3A B:HEM201 4.3 12.2 1.0 C2B B:HEM201 4.3 12.8 1.0 C3B B:HEM201 4.3 12.8 1.0 ND1 B:HIS89 4.3 21.7 1.0 C3D B:HEM201 4.3 21.4 1.0 C2D B:HEM201 4.3 13.1 1.0 CG B:HIS89 4.4 22.0 1.0 O10 B:4NC202 4.6 24.8 1.0 C6 B:4NC202 4.8 20.1 1.0 CG1 B:VAL59 4.8 10.1 1.0 CE B:MET86 5.0 21.4 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