Iron in PDB 3waq: Hemerythrin-Like Domain of Dcrh I119E Mutant (Met)

The structure of Hemerythrin-Like Domain of Dcrh I119E Mutant (Met), PDB code: 3waq 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)	19.71 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.965, 50.859, 76.677, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.1

The binding sites of Iron atom in the Hemerythrin-Like Domain of Dcrh I119E Mutant (Met) (pdb code 3waq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Hemerythrin-Like Domain of Dcrh I119E Mutant (Met), PDB code: 3waq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Hemerythrin-Like Domain of Dcrh I119E 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 I119E Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:13.6 occ:1.00 FE1 A:FEO201 0.0 13.6 1.0 O A:FEO201 1.8 14.0 1.0 NE2 A:HIS118 2.1 14.8 1.0 OE1 A:GLU63 2.1 13.3 1.0 NE2 A:HIS78 2.3 17.5 1.0 OD1 A:ASP123 2.3 12.8 1.0 NE2 A:HIS82 2.3 15.7 1.0 CE1 A:HIS118 3.0 13.3 1.0 CD A:GLU63 3.1 10.8 1.0 CD2 A:HIS118 3.1 15.5 1.0 CE1 A:HIS82 3.1 12.3 1.0 CE1 A:HIS78 3.2 12.4 1.0 CG A:ASP123 3.2 10.8 1.0 FE2 A:FEO201 3.2 12.9 1.0 CD2 A:HIS78 3.3 14.2 1.0 CD2 A:HIS82 3.3 14.4 1.0 OE2 A:GLU63 3.4 12.3 1.0 OD2 A:ASP123 3.4 11.2 1.0 ND1 A:HIS118 4.1 17.4 1.0 CG A:HIS118 4.2 14.8 1.0 ND1 A:HIS82 4.3 15.4 1.0 ND1 A:HIS78 4.3 15.1 1.0 CG A:HIS78 4.4 17.1 1.0 CG A:GLU63 4.4 12.8 1.0 CG A:HIS82 4.4 14.6 1.0 NE2 A:HIS59 4.5 11.3 1.0 OE1 A:GLU119 4.5 15.4 1.0 CB A:ASP123 4.6 12.1 1.0 CE2 A:TYR126 4.7 14.2 1.0 CD1 A:PHE60 4.7 11.8 1.0 CE1 A:PHE60 4.8 13.9 1.0 CB A:GLU63 4.8 14.4 1.0

Iron binding site 2 out of 2 in the Hemerythrin-Like Domain of Dcrh I119E 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 I119E Mutant (Met) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.9 occ:1.00 FE2 A:FEO201 0.0 12.9 1.0 O A:FEO201 1.8 14.0 1.0 OD2 A:ASP123 2.0 11.2 1.0 OE1 A:GLU119 2.1 15.4 1.0 NE2 A:HIS59 2.1 11.3 1.0 OE2 A:GLU63 2.3 12.3 1.0 NE2 A:HIS23 2.4 13.0 1.0 CE1 A:HIS59 2.9 12.5 1.0 CG A:ASP123 3.0 10.8 1.0 CD A:GLU119 3.1 16.7 1.0 CD A:GLU63 3.1 10.8 1.0 CD2 A:HIS59 3.2 13.2 1.0 FE1 A:FEO201 3.2 13.6 1.0 CE1 A:HIS23 3.3 14.3 1.0 CD2 A:HIS23 3.3 11.3 1.0 OD1 A:ASP123 3.4 12.8 1.0 OE1 A:GLU63 3.4 13.3 1.0 OE2 A:GLU119 3.5 15.5 1.0 ND1 A:HIS59 4.1 13.5 1.0 CD2 A:HIS118 4.2 15.5 1.0 CG A:HIS59 4.3 13.2 1.0 CB A:ASP123 4.3 12.1 1.0 NE2 A:HIS118 4.3 14.8 1.0 CG A:GLU63 4.3 12.8 1.0 OH A:TYR126 4.4 12.1 1.0 CG A:GLU119 4.4 17.9 1.0 ND1 A:HIS23 4.4 16.4 1.0 CA A:GLU119 4.4 13.4 1.0 CG A:HIS23 4.5 13.9 1.0 CB A:GLU119 4.6 16.7 1.0 NE2 A:HIS82 4.7 15.7 1.0 CE1 A:PHE60 4.9 13.9 1.0 O A:GLU119 5.0 14.2 1.0

Y.Okamoto, A.Onoda, H.Sugimoto, Y.Takano, S.Hirota, D.M.Kurtz Jr., Y.Shiro, T.Hayashi. Crystal Structure, Exogenous Ligand Binding, and Redox Properties of An Engineered Diiron Active Site in A Bacterial Hemerythrin Inorg.Chem. V. 52 13014 2013.
ISSN: ISSN 0020-1669
PubMed: 24187962
DOI: 10.1021/IC401632X