Iron in PDB 7m1k: Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol

The structure of Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol, PDB code: 7m1k 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)	37.12 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.145, 66.697, 68.028, 90, 90, 90
R / Rfree (%)	17.1 / 22.3

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

Fluorine

(F)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase B in Complex with 2,6- Difluorophenol (pdb code 7m1k). 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- Difluorophenol, PDB code: 7m1k:
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- Difluorophenol


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- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:37.3 occ:1.00 FE A:HEM201 0.0 37.3 1.0 ND A:HEM201 1.9 26.5 1.0 NA A:HEM201 2.0 31.7 1.0 NC A:HEM201 2.1 33.2 1.0 NB A:HEM201 2.1 33.8 1.0 NE2 A:HIS89 2.4 40.7 1.0 C1D A:HEM201 2.9 33.4 1.0 C4D A:HEM201 2.9 26.6 1.0 C1A A:HEM201 3.0 31.0 1.0 C4A A:HEM201 3.0 29.8 1.0 C4C A:HEM201 3.1 37.4 1.0 C1B A:HEM201 3.1 32.0 1.0 C4B A:HEM201 3.1 34.4 1.0 C1C A:HEM201 3.2 36.1 1.0 CE1 A:HIS89 3.3 43.9 1.0 CD2 A:HIS89 3.4 42.1 1.0 CHA A:HEM201 3.4 27.3 1.0 CHD A:HEM201 3.4 34.4 1.0 CHB A:HEM201 3.4 31.8 1.0 CHC A:HEM201 3.6 34.5 1.0 NE2 A:HIS55 3.8 34.0 1.0 CG2 A:VAL59 3.9 22.3 1.0 C2A A:HEM201 4.1 32.1 1.0 C3A A:HEM201 4.2 31.9 1.0 C2D A:HEM201 4.2 31.0 1.0 C3D A:HEM201 4.2 31.3 1.0 C3C A:HEM201 4.3 37.4 1.0 CE1 A:HIS55 4.3 33.5 1.0 C2C A:HEM201 4.3 37.6 1.0 C2B A:HEM201 4.3 32.9 1.0 C3B A:HEM201 4.4 32.0 1.0 ND1 A:HIS89 4.4 45.9 1.0 CG A:HIS89 4.5 42.4 1.0 CE A:MET86 4.7 37.0 1.0 CD2 A:HIS55 4.9 34.5 1.0 CD1 A:LEU92 5.0 41.8 1.0

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


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- Difluorophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:20.7 occ:1.00 FE B:HEM202 0.0 20.7 1.0 ND B:HEM202 2.0 21.3 1.0 NA B:HEM202 2.0 19.8 1.0 NC B:HEM202 2.1 21.0 1.0 NB B:HEM202 2.1 19.6 1.0 NE2 B:HIS89 2.2 21.8 1.0 O B:HOH301 2.4 6.5 0.2 C1D B:HEM202 3.0 22.1 1.0 C4D B:HEM202 3.0 22.5 1.0 C1A B:HEM202 3.0 21.8 1.0 C4A B:HEM202 3.0 20.1 1.0 C1B B:HEM202 3.0 19.6 1.0 C4C B:HEM202 3.1 23.0 1.0 C4B B:HEM202 3.1 19.6 1.0 C1C B:HEM202 3.1 21.3 1.0 CE1 B:HIS89 3.2 23.8 1.0 CD2 B:HIS89 3.3 21.5 1.0 CHB B:HEM202 3.4 20.6 1.0 CHD B:HEM202 3.4 23.2 1.0 CHA B:HEM202 3.5 21.9 1.0 CHC B:HEM202 3.5 21.1 1.0 C2A B:HEM202 4.2 21.0 1.0 C3A B:HEM202 4.2 21.2 1.0 CG2 B:VAL59 4.2 16.5 1.0 C2D B:HEM202 4.3 24.4 1.0 C2B B:HEM202 4.3 18.9 1.0 C3C B:HEM202 4.3 22.8 1.0 C2C B:HEM202 4.3 22.0 1.0 C3D B:HEM202 4.3 25.7 1.0 C3B B:HEM202 4.3 18.6 1.0 ND1 B:HIS89 4.3 21.9 1.0 CG B:HIS89 4.4 22.4 1.0 O B:FFP204 4.5 28.0 0.8 F2 B:FFP204 4.8 32.6 0.8 CG1 B:VAL59 4.8 16.2 1.0 CE B:MET86 5.0 25.1 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