Iron in PDB 7m1i: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol, PDB code: 7m1i 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)	37.15 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.84, 67.31, 68.03, 90, 90, 90
R / Rfree (%)	18.6 / 24.1

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

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Dichlorophenol (pdb code 7m1i). 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- Dichlorophenol, PDB code: 7m1i:
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- Dichlorophenol


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- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.8 occ:1.00 FE A:HEM201 0.0 27.8 1.0 ND A:HEM201 1.9 25.6 1.0 NA A:HEM201 2.0 28.6 1.0 NC A:HEM201 2.1 27.1 1.0 NB A:HEM201 2.1 25.9 1.0 NE2 A:HIS89 2.3 27.9 1.0 C1D A:HEM201 2.9 28.2 1.0 C4D A:HEM201 3.0 29.0 1.0 C1A A:HEM201 3.0 29.7 1.0 C4A A:HEM201 3.0 27.1 1.0 C1B A:HEM201 3.1 24.4 1.0 C4C A:HEM201 3.1 28.0 1.0 C4B A:HEM201 3.1 27.3 1.0 C1C A:HEM201 3.1 28.0 1.0 CE1 A:HIS89 3.2 28.8 1.0 CD2 A:HIS89 3.3 30.5 1.0 CHD A:HEM201 3.4 28.0 1.0 CHA A:HEM201 3.4 29.4 1.0 CHB A:HEM201 3.4 25.1 1.0 CHC A:HEM201 3.5 25.1 1.0 C04 A:DUB202 4.0 76.1 0.8 CG2 A:VAL59 4.2 25.1 1.0 C2A A:HEM201 4.2 31.4 1.0 C3A A:HEM201 4.2 28.8 1.0 C2D A:HEM201 4.2 31.3 1.0 C3D A:HEM201 4.2 33.4 1.0 C3C A:HEM201 4.3 26.8 1.0 C2C A:HEM201 4.3 27.1 1.0 C2B A:HEM201 4.3 24.8 1.0 ND1 A:HIS89 4.4 30.4 1.0 C3B A:HEM201 4.4 24.8 1.0 CG A:HIS89 4.4 29.6 1.0 C05 A:DUB202 4.5 75.7 0.8 CE A:MET86 4.6 35.3 1.0 CG1 A:VAL59 4.8 24.8 1.0

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


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- Dichlorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:38.3 occ:1.00 FE B:HEM201 0.0 38.3 1.0 ND B:HEM201 1.9 40.1 1.0 NA B:HEM201 2.0 39.2 1.0 NC B:HEM201 2.1 41.5 1.0 NB B:HEM201 2.1 37.4 0.8 NE2 B:HIS89 2.1 48.7 1.0 C1D B:HEM201 2.9 40.4 1.0 C4D B:HEM201 2.9 42.6 1.0 CD2 B:HIS89 3.0 49.6 1.0 C1A B:HEM201 3.0 43.3 1.0 C4C B:HEM201 3.1 43.1 1.0 C4A B:HEM201 3.1 40.5 1.0 C1B B:HEM201 3.1 37.3 1.0 C4B B:HEM201 3.1 36.3 0.4 C1C B:HEM201 3.2 43.8 1.0 CE1 B:HIS89 3.2 54.1 1.0 CHD B:HEM201 3.4 40.2 1.0 CHA B:HEM201 3.4 42.3 1.0 CHB B:HEM201 3.5 38.4 1.0 CHC B:HEM201 3.5 40.0 1.0 CG2 B:VAL59 3.9 24.7 1.0 C04 B:DUB202 4.1 47.8 0.8 C2D B:HEM201 4.2 43.9 1.0 CG B:HIS89 4.2 49.9 1.0 C3D B:HEM201 4.2 46.8 1.0 C2A B:HEM201 4.2 44.2 1.0 C3A B:HEM201 4.2 41.4 1.0 ND1 B:HIS89 4.3 48.3 1.0 C3C B:HEM201 4.3 45.3 1.0 C2B B:HEM201 4.3 35.2 1.0 C2C B:HEM201 4.3 45.4 1.0 C3B B:HEM201 4.4 34.6 0.3 CG1 B:VAL59 4.5 23.2 1.0 C03 B:DUB202 4.5 49.7 0.8 CB B:VAL59 4.7 22.3 1.0

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