Iron in PDB 5v5j: Oxyferrous Dehaloperoxidase B

The structure of Oxyferrous Dehaloperoxidase B, PDB code: 5v5j was solved by L.M.Carey, R.A.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.581, 67.018, 68.448, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.5

The binding sites of Iron atom in the Oxyferrous Dehaloperoxidase B (pdb code 5v5j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Oxyferrous Dehaloperoxidase B, PDB code: 5v5j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Oxyferrous Dehaloperoxidase B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxyferrous Dehaloperoxidase B within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:21.4 occ:1.00 FE A:HEM201 0.0 21.4 1.0 NC A:HEM201 2.0 20.6 1.0 ND A:HEM201 2.1 21.5 1.0 NA A:HEM201 2.1 18.8 1.0 NB A:HEM201 2.1 18.8 1.0 NE2 A:HIS89 2.3 22.3 1.0 O2 A:OXY204 2.4 27.7 1.0 C4C A:HEM201 3.0 23.8 1.0 C1D A:HEM201 3.1 23.0 1.0 C4A A:HEM201 3.1 15.1 1.0 C1B A:HEM201 3.1 18.6 1.0 C1A A:HEM201 3.1 21.1 1.0 C1C A:HEM201 3.1 20.0 1.0 C4D A:HEM201 3.1 22.5 1.0 C4B A:HEM201 3.1 20.4 1.0 CD2 A:HIS89 3.2 27.8 1.0 CE1 A:HIS89 3.4 25.2 1.0 CHD A:HEM201 3.4 21.6 1.0 CHB A:HEM201 3.4 15.8 1.0 CHC A:HEM201 3.5 23.4 1.0 CHA A:HEM201 3.5 23.7 1.0 O1 A:OXY204 3.6 35.2 1.0 C3C A:HEM201 4.3 22.1 1.0 C3A A:HEM201 4.3 19.4 1.0 C2D A:HEM201 4.3 19.4 1.0 C2A A:HEM201 4.3 18.6 1.0 C2C A:HEM201 4.3 21.2 1.0 C3D A:HEM201 4.3 20.9 1.0 C2B A:HEM201 4.3 17.6 1.0 C3B A:HEM201 4.3 20.3 1.0 CG2 A:VAL59 4.4 17.5 1.0 CG A:HIS89 4.4 19.1 1.0 ND1 A:HIS89 4.4 22.6 1.0 CE1 A:HIS55 4.8 18.6 1.0 CE A:MET86 4.9 19.2 1.0

Iron binding site 2 out of 2 in the Oxyferrous Dehaloperoxidase B


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxyferrous Dehaloperoxidase B within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:21.2 occ:1.00 FE B:HEM201 0.0 21.2 1.0 NA B:HEM201 2.0 16.0 1.0 ND B:HEM201 2.0 21.3 1.0 NB B:HEM201 2.0 19.3 1.0 NC B:HEM201 2.0 24.1 1.0 NE2 B:HIS89 2.3 21.3 1.0 O1 B:OXY202 2.5 26.4 1.0 C4A B:HEM201 3.0 18.6 1.0 C1D B:HEM201 3.0 27.0 1.0 C1B B:HEM201 3.0 21.0 1.0 C4C B:HEM201 3.1 24.0 1.0 C1A B:HEM201 3.1 24.6 1.0 C1C B:HEM201 3.1 22.6 1.0 C4B B:HEM201 3.1 23.2 1.0 C4D B:HEM201 3.1 28.4 1.0 CD2 B:HIS89 3.2 23.4 1.0 CE1 B:HIS89 3.3 26.0 1.0 CHD B:HEM201 3.4 24.5 1.0 CHB B:HEM201 3.4 17.3 1.0 CHC B:HEM201 3.5 23.2 1.0 CHA B:HEM201 3.5 22.6 1.0 O2 B:OXY202 3.7 32.9 1.0 CG2 B:VAL59 4.2 15.8 1.0 C3A B:HEM201 4.3 21.6 1.0 C2D B:HEM201 4.3 22.3 1.0 C2A B:HEM201 4.3 23.5 1.0 C2B B:HEM201 4.3 15.3 1.0 C3C B:HEM201 4.3 20.2 1.0 C2C B:HEM201 4.3 24.4 1.0 C3D B:HEM201 4.3 24.9 1.0 C3B B:HEM201 4.3 19.4 1.0 CG B:HIS89 4.4 22.2 1.0 ND1 B:HIS89 4.4 18.5 1.0 CE1 B:HIS55 4.8 33.5 1.0 CE B:MET86 4.9 22.9 1.0 CG1 B:VAL59 5.0 21.5 1.0

L.M.Carey, R.Gavenko, D.A.Svistunenko, R.A.Ghiladi. How Nature Tunes Isoenzyme Activity in the Multifunctional Catalytic Globin Dehaloperoxidase From Amphitrite Ornata. Biochim Biophys Acta V.1866 230 2018PROTEINS Proteom.
ISSN: ISSN 1570-9639
PubMed: 29128676
DOI: 10.1016/J.BBAPAP.2017.11.004