Iron in PDB 3agu: Hemerythrin-Like Domain of Dcrh (Semimet-R)

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R), PDB code: 3agu was solved by A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, 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 / 1.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.425, 44.903, 48.076, 95.21, 103.98, 89.95
R / Rfree (%)	24.7 / 29.2

The structure of Hemerythrin-Like Domain of Dcrh (Semimet-R) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Hemerythrin-Like Domain of Dcrh (Semimet-R) (pdb code 3agu). 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 (Semimet-R), PDB code: 3agu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


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 (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:8.9 occ:1.00 FE2 A:CFO201 0.0 8.9 1.0 O A:CFO201 2.0 5.7 1.0 OD2 A:ASP123 2.2 7.3 1.0 NE2 A:HIS59 2.2 8.4 1.0 CL A:CFO201 2.4 11.2 1.0 OE2 A:GLU63 2.4 5.8 1.0 NE2 A:HIS23 2.4 9.2 1.0 CG A:ASP123 3.1 8.4 1.0 CE1 A:HIS59 3.2 7.6 1.0 CD A:GLU63 3.2 7.3 1.0 CD2 A:HIS59 3.2 6.4 1.0 CD2 A:HIS23 3.3 7.3 1.0 FE1 A:CFO201 3.3 6.9 1.0 OD1 A:ASP123 3.4 9.8 1.0 CE1 A:HIS23 3.4 9.5 1.0 OE1 A:GLU63 3.5 6.6 1.0 CD2 A:HIS118 3.9 9.0 1.0 NE2 A:HIS118 4.2 9.9 1.0 ND1 A:HIS59 4.3 6.5 1.0 CG A:HIS59 4.4 8.2 1.0 CB A:ASP123 4.4 9.9 1.0 OH A:TYR126 4.4 8.6 1.0 CG A:GLU63 4.5 8.0 1.0 CG A:HIS23 4.5 8.2 1.0 ND1 A:HIS23 4.5 7.9 1.0 CG1 A:ILE119 4.6 8.2 1.0 CE1 A:PHE60 4.7 8.9 1.0 NE2 A:HIS82 4.8 9.8 1.0 CD1 A:PHE60 4.9 8.0 1.0

Iron binding site 2 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


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 (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:6.9 occ:1.00 FE1 A:CFO201 0.0 6.9 1.0 O A:CFO201 2.0 5.7 1.0 OE1 A:GLU63 2.2 6.6 1.0 NE2 A:HIS118 2.2 9.9 1.0 NE2 A:HIS78 2.2 5.8 1.0 NE2 A:HIS82 2.3 9.8 1.0 OD1 A:ASP123 2.3 9.8 1.0 CE1 A:HIS82 3.1 8.2 1.0 CD A:GLU63 3.1 7.3 1.0 CD2 A:HIS118 3.1 9.0 1.0 CE1 A:HIS78 3.2 6.1 1.0 CE1 A:HIS118 3.2 9.2 1.0 CD2 A:HIS78 3.2 8.2 1.0 CG A:ASP123 3.2 8.4 1.0 CD2 A:HIS82 3.3 9.7 1.0 FE2 A:CFO201 3.3 8.9 1.0 OE2 A:GLU63 3.4 5.8 1.0 OD2 A:ASP123 3.5 7.3 1.0 ND1 A:HIS82 4.3 11.1 1.0 CG A:HIS118 4.3 9.8 1.0 ND1 A:HIS118 4.3 9.6 1.0 ND1 A:HIS78 4.3 9.4 1.0 CG A:HIS78 4.4 9.2 1.0 CG A:HIS82 4.4 9.6 1.0 CG A:GLU63 4.5 8.0 1.0 CE2 A:TYR126 4.6 7.7 1.0 CB A:ASP123 4.6 9.9 1.0 CL A:CFO201 4.7 11.2 1.0 CD1 A:PHE60 4.8 8.0 1.0 CB A:GLU63 4.8 10.0 1.0 NE2 A:HIS59 4.8 8.4 1.0 CE1 A:PHE60 4.8 8.9 1.0 CA A:ASP123 4.9 9.8 1.0 N A:ASP123 4.9 10.6 1.0

Iron binding site 3 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


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 (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.3 occ:1.00 FE2 B:CFO201 0.0 9.3 1.0 O B:CFO201 2.0 7.1 1.0 OD2 B:ASP123 2.0 6.7 1.0 NE2 B:HIS59 2.3 8.1 1.0 NE2 B:HIS23 2.3 9.2 1.0 CL B:CFO201 2.4 10.5 1.0 OE2 B:GLU63 2.4 5.3 1.0 CG B:ASP123 3.0 8.7 1.0 CE1 B:HIS59 3.2 7.0 1.0 CD2 B:HIS23 3.2 7.5 1.0 CD B:GLU63 3.3 7.2 1.0 FE1 B:CFO201 3.3 7.8 1.0 CD2 B:HIS59 3.3 6.5 1.0 OD1 B:ASP123 3.3 9.1 1.0 CE1 B:HIS23 3.4 9.2 1.0 OE1 B:GLU63 3.6 6.5 1.0 CD2 B:HIS118 4.0 8.9 1.0 NE2 B:HIS118 4.3 10.8 1.0 CB B:ASP123 4.3 9.8 1.0 ND1 B:HIS59 4.4 6.4 1.0 CG B:HIS23 4.4 8.6 1.0 OH B:TYR126 4.4 8.1 1.0 ND1 B:HIS23 4.5 8.2 1.0 CG B:HIS59 4.5 7.8 1.0 CG B:GLU63 4.5 7.8 1.0 CG1 B:ILE119 4.6 8.6 1.0 CE1 B:PHE60 4.7 8.2 1.0 NE2 B:HIS82 4.8 8.7 1.0 CD1 B:PHE60 4.9 7.9 1.0

Iron binding site 4 out of 4 in the Hemerythrin-Like Domain of Dcrh (Semimet-R)


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 (Semimet-R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:7.8 occ:1.00 FE1 B:CFO201 0.0 7.8 1.0 O B:CFO201 2.0 7.1 1.0 OE1 B:GLU63 2.1 6.5 1.0 OD1 B:ASP123 2.2 9.1 1.0 NE2 B:HIS118 2.2 10.8 1.0 NE2 B:HIS82 2.3 8.7 1.0 NE2 B:HIS78 2.3 6.0 1.0 CD B:GLU63 3.1 7.2 1.0 CE1 B:HIS82 3.1 7.7 1.0 CD2 B:HIS118 3.1 8.9 1.0 CG B:ASP123 3.2 8.7 1.0 CD2 B:HIS78 3.2 8.2 1.0 CE1 B:HIS118 3.3 9.0 1.0 CE1 B:HIS78 3.3 5.8 1.0 FE2 B:CFO201 3.3 9.3 1.0 CD2 B:HIS82 3.3 9.3 1.0 OE2 B:GLU63 3.4 5.3 1.0 OD2 B:ASP123 3.4 6.7 1.0 ND1 B:HIS82 4.3 10.3 1.0 CG B:HIS118 4.3 9.7 1.0 ND1 B:HIS118 4.3 9.6 1.0 ND1 B:HIS78 4.4 9.4 1.0 CG B:HIS78 4.4 8.3 1.0 CG B:HIS82 4.4 8.8 1.0 CG B:GLU63 4.5 7.8 1.0 CE2 B:TYR126 4.5 6.8 1.0 CB B:ASP123 4.6 9.8 1.0 CL B:CFO201 4.7 10.5 1.0 CD1 B:PHE60 4.7 7.9 1.0 CB B:GLU63 4.8 9.4 1.0 CE1 B:PHE60 4.8 8.2 1.0 NE2 B:HIS59 4.8 8.1 1.0 CA B:ASP123 4.9 9.7 1.0 N B:ASP123 5.0 11.0 1.0

A.Onoda, Y.Okamoto, H.Sugimoto, E.Mizohata, T.Inoue, Y.Shiro, T.Hayashi. Characteristics of Diiron Site with Large Cavity in Hemerythrin-Like Domain of Dcrh To Be Published.