Iron in PDB 7m1j: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j 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)	30.40 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.756, 66.594, 68.283, 90, 90, 90
R / Rfree (%)	14.6 / 20.6

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol (pdb code 7m1j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol, PDB code: 7m1j:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:34.7 occ:1.00 FE A:HEM201 0.0 34.7 1.0 ND A:HEM201 1.9 36.3 1.0 NA A:HEM201 2.0 33.8 1.0 NE2 A:HIS89 2.0 38.2 1.0 NB A:HEM201 2.1 77.8 1.0 NC A:HEM201 2.1 36.0 1.0 NE2 A:HIS55 2.2 41.2 0.7 C4D A:HEM201 2.8 37.8 1.0 C1D A:HEM201 2.9 38.0 1.0 C1A A:HEM201 3.0 35.8 1.0 CD2 A:HIS89 3.0 52.3 1.0 C1B A:HEM201 3.1 38.7 1.0 C4C A:HEM201 3.1 37.0 1.0 CE1 A:HIS89 3.1 48.0 1.0 C4A A:HEM201 3.1 33.3 1.0 C4B A:HEM201 3.1 35.6 1.0 CD2 A:HIS55 3.1 23.2 0.7 CE1 A:HIS55 3.2 26.0 0.7 C1C A:HEM201 3.2 44.5 1.0 CHA A:HEM201 3.3 39.6 1.0 CHD A:HEM201 3.4 38.1 1.0 CHB A:HEM201 3.5 35.3 1.0 CHC A:HEM201 3.6 39.3 1.0 C3D A:HEM201 4.1 35.3 1.0 C2D A:HEM201 4.1 37.7 1.0 CG A:HIS89 4.1 40.8 1.0 ND1 A:HIS89 4.2 46.0 1.0 C2A A:HEM201 4.2 49.9 1.0 ND1 A:HIS55 4.3 20.5 0.7 CG A:HIS55 4.3 21.5 0.7 C3A A:HEM201 4.3 43.9 1.0 C2B A:HEM201 4.3 36.4 1.0 C3C A:HEM201 4.3 38.5 1.0 C2C A:HEM201 4.4 42.0 1.0 CG2 A:VAL59 4.4 21.9 1.0 C3B A:HEM201 4.4 37.4 1.0 CD1 A:LEU92 4.9 48.8 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dibromophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:20.2 occ:1.00 FE B:HEM201 0.0 20.2 1.0 ND B:HEM201 2.0 21.9 1.0 NA B:HEM201 2.0 19.7 1.0 NB B:HEM201 2.1 15.9 1.0 NC B:HEM201 2.1 21.0 1.0 NE2 B:HIS89 2.1 20.5 1.0 C B:94N202 2.3 25.3 0.7 C1 B:94N202 2.8 44.7 0.7 C1D B:HEM201 3.0 20.8 1.0 C1B B:HEM201 3.1 16.4 1.0 C4B B:HEM201 3.1 16.8 1.0 C1A B:HEM201 3.1 21.2 1.0 C4C B:HEM201 3.1 21.2 1.0 C4A B:HEM201 3.1 18.0 1.0 C4D B:HEM201 3.1 21.4 1.0 C1C B:HEM201 3.1 19.4 1.0 CE1 B:HIS89 3.1 27.5 1.0 CD2 B:HIS89 3.2 23.4 1.0 CHD B:HEM201 3.4 20.0 1.0 C5 B:94N202 3.4 41.1 0.7 CHB B:HEM201 3.5 17.1 1.0 CHC B:HEM201 3.5 17.9 1.0 CHA B:HEM201 3.6 21.4 1.0 C2 B:94N202 4.2 56.7 0.7 ND1 B:HIS89 4.2 23.2 1.0 C2D B:HEM201 4.3 24.3 1.0 C2A B:HEM201 4.3 18.4 1.0 C3A B:HEM201 4.3 18.1 1.0 C3C B:HEM201 4.3 20.2 1.0 C2B B:HEM201 4.3 17.4 1.0 CG B:HIS89 4.3 23.4 1.0 C3D B:HEM201 4.3 25.2 1.0 C2C B:HEM201 4.3 20.2 1.0 C3B B:HEM201 4.3 18.2 1.0 CG2 B:VAL59 4.4 18.7 1.0 C4 B:94N202 4.6 51.8 0.7 CG1 B:VAL59 4.7 18.2 1.0 CE B:MET86 4.9 20.2 1.0 C3 B:94N202 5.0 53.6 0.7

T.Malewschik, L.M.Carey, V.De Serrano, R.A.Ghiladi. Bridging the Functional Gap Between Reactivity and Inhibition in Dehaloperoxidase B From Amphitrite Ornata: Mechanistic and Structural Studies with 2,4- and 2,6-Dihalophenols. J.Inorg.Biochem. V. 236 11944 2022.
ISSN: ISSN 0162-0134
PubMed: 35969974
DOI: 10.1016/J.JINORGBIO.2022.111944