Iron in PDB 3whn: Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)

The structure of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met), PDB code: 3whn was solved by Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr., Y.Shiro, T.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.573, 44.082, 46.715, 92.71, 102.59, 90.02
R / Rfree (%)	19.3 / 24.8

The structure of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Iron atom in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) (pdb code 3whn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met), PDB code: 3whn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:7.5 occ:1.00 FE2 A:CFO201 0.0 7.5 1.0 O A:CFO201 1.9 7.0 1.0 OD2 A:ASP123 2.2 7.7 1.0 NE2 A:HIS59 2.2 4.5 1.0 NE2 A:HIS23 2.3 5.7 1.0 CL A:CFO201 2.4 8.1 1.0 OE2 A:GLU63 2.5 4.2 1.0 CG A:ASP123 3.1 7.8 1.0 CE1 A:HIS59 3.1 4.5 1.0 CD2 A:HIS59 3.2 4.5 1.0 FE1 A:CFO201 3.2 7.7 1.0 CD2 A:HIS23 3.3 5.7 1.0 CE1 A:HIS23 3.3 5.5 1.0 CD A:GLU63 3.3 4.2 1.0 OD1 A:ASP123 3.5 7.5 1.0 OE1 A:GLU63 3.6 4.2 1.0 CD2 A:HIS119 4.0 8.2 1.0 NE2 A:HIS119 4.2 8.0 1.0 ND1 A:HIS59 4.3 4.4 1.0 CG A:HIS59 4.4 4.7 1.0 CB A:ASP123 4.4 8.6 1.0 ND1 A:HIS23 4.4 5.8 1.0 CG A:HIS23 4.4 5.7 1.0 CE1 A:PHE60 4.6 6.2 1.0 CG A:GLU63 4.6 4.4 1.0 OH A:TYR126 4.6 6.4 1.0 CG A:MET120 4.7 9.0 1.0 CD1 A:PHE60 4.7 6.2 1.0 NE2 A:HIS82 4.8 5.7 1.0

Iron binding site 2 out of 4 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:7.7 occ:1.00 FE1 A:CFO201 0.0 7.7 1.0 O A:CFO201 1.9 7.0 1.0 OE1 A:GLU63 2.1 4.2 1.0 NE2 A:HIS119 2.2 8.0 1.0 NE2 A:HIS82 2.2 5.7 1.0 OD1 A:ASP123 2.3 7.5 1.0 NE2 A:HIS78 2.4 7.1 1.0 CD A:GLU63 3.0 4.2 1.0 CE1 A:HIS82 3.1 5.7 1.0 CD2 A:HIS119 3.1 8.2 1.0 CE1 A:HIS119 3.2 8.1 1.0 CG A:ASP123 3.2 7.8 1.0 FE2 A:CFO201 3.2 7.5 1.0 OE2 A:GLU63 3.3 4.2 1.0 CE1 A:HIS78 3.3 6.9 1.0 CD2 A:HIS82 3.3 5.7 1.0 OD2 A:ASP123 3.4 7.7 1.0 CD2 A:HIS78 3.4 7.0 1.0 ND1 A:HIS82 4.3 5.9 1.0 ND1 A:HIS119 4.3 8.0 1.0 CG A:HIS119 4.3 8.3 1.0 CG A:GLU63 4.4 4.4 1.0 CG A:HIS82 4.4 5.8 1.0 ND1 A:HIS78 4.5 7.2 1.0 CD1 A:PHE60 4.5 6.2 1.0 CE1 A:PHE60 4.5 6.2 1.0 CG A:HIS78 4.6 7.0 1.0 CB A:ASP123 4.6 8.6 1.0 NE2 A:HIS59 4.6 4.5 1.0 CE2 A:TYR126 4.7 6.8 1.0 CL A:CFO201 4.7 8.1 1.0 CB A:GLU63 4.8 4.5 1.0

Iron binding site 3 out of 4 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:7.5 occ:1.00 FE2 B:CFO201 0.0 7.5 1.0 O B:CFO201 1.9 7.4 1.0 OD2 B:ASP123 2.1 9.2 1.0 NE2 B:HIS59 2.2 4.7 1.0 NE2 B:HIS23 2.4 6.4 1.0 CL B:CFO201 2.4 7.8 1.0 OE2 B:GLU63 2.6 5.0 1.0 CE1 B:HIS59 3.0 4.7 1.0 CG B:ASP123 3.1 9.0 1.0 CD2 B:HIS59 3.2 4.6 1.0 FE1 B:CFO201 3.2 8.2 1.0 CD2 B:HIS23 3.3 6.5 1.0 CD B:GLU63 3.4 4.9 1.0 CE1 B:HIS23 3.4 6.4 1.0 OD1 B:ASP123 3.4 8.2 1.0 OE1 B:GLU63 3.6 5.0 1.0 CD2 B:HIS119 4.0 8.1 1.0 ND1 B:HIS59 4.2 4.8 1.0 NE2 B:HIS119 4.2 8.0 1.0 CG B:HIS59 4.3 4.8 1.0 CB B:ASP123 4.3 9.4 1.0 ND1 B:HIS23 4.5 6.4 1.0 CG B:HIS23 4.5 6.5 1.0 CG B:GLU63 4.5 4.9 1.0 OH B:TYR126 4.6 8.2 1.0 CE1 B:PHE60 4.6 6.5 1.0 NE2 B:HIS82 4.8 6.7 1.0 CD1 B:PHE60 4.8 6.4 1.0 CG B:MET120 4.9 9.6 1.0

Iron binding site 4 out of 4 in the Hemerythrin-Like Domain of Dcrh I119H Mutant (Met)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hemerythrin-Like Domain of Dcrh I119H Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:8.2 occ:1.00 FE1 B:CFO201 0.0 8.2 1.0 O B:CFO201 1.9 7.4 1.0 OE1 B:GLU63 2.2 5.0 1.0 NE2 B:HIS119 2.2 8.0 1.0 NE2 B:HIS82 2.2 6.7 1.0 OD1 B:ASP123 2.2 8.2 1.0 NE2 B:HIS78 2.4 8.5 1.0 CD B:GLU63 3.1 4.9 1.0 CD2 B:HIS119 3.1 8.1 1.0 CE1 B:HIS82 3.1 6.4 1.0 CG B:ASP123 3.2 9.0 1.0 FE2 B:CFO201 3.2 7.5 1.0 CE1 B:HIS119 3.2 8.3 1.0 CD2 B:HIS82 3.3 6.6 1.0 OE2 B:GLU63 3.3 5.0 1.0 CD2 B:HIS78 3.3 8.4 1.0 CE1 B:HIS78 3.4 8.3 1.0 OD2 B:ASP123 3.4 9.2 1.0 ND1 B:HIS82 4.3 6.5 1.0 CG B:HIS119 4.3 8.1 1.0 ND1 B:HIS119 4.3 8.2 1.0 CG B:HIS82 4.4 6.6 1.0 CG B:GLU63 4.4 4.9 1.0 CD1 B:PHE60 4.5 6.4 1.0 ND1 B:HIS78 4.5 8.4 1.0 CG B:HIS78 4.5 8.2 1.0 CE1 B:PHE60 4.6 6.5 1.0 CB B:ASP123 4.6 9.4 1.0 NE2 B:HIS59 4.6 4.7 1.0 CE2 B:TYR126 4.7 8.4 1.0 CL B:CFO201 4.7 7.8 1.0 CB B:GLU63 4.8 5.0 1.0

Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr., Y.Shiro, T.Hayashi. H2O2-Dependent Substrate Oxidation By An Engineered Diiron Site in A Bacterial Hemerythrin Chem.Commun.(Camb.) 2014.
ISSN: ESSN 1364-548X
PubMed: 24400317
DOI: 10.1039/C3CC48108E