Iron in PDB 3i8r: Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt)

The structure of Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt), PDB code: 3i8r was solved by T.Matsui, M.Unno, M.Ikeda-Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.117, 62.563, 108.002, 90.00, 100.67, 90.00
R / Rfree (%)	19.4 / 22.4

The binding sites of Iron atom in the Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt) (pdb code 3i8r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt), PDB code: 3i8r:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt)


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 the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:19.8 occ:1.00 FE A:HEM901 0.0 19.8 1.0 NE2 A:HIS20 2.0 18.2 1.0 NC A:HEM901 2.0 18.0 1.0 ND A:HEM901 2.0 17.3 1.0 NA A:HEM901 2.0 17.1 1.0 NB A:HEM901 2.1 18.9 1.0 S4 A:DTV2001 2.3 21.2 1.0 CE1 A:HIS20 3.0 25.7 1.0 CD2 A:HIS20 3.0 18.4 1.0 C4D A:HEM901 3.0 19.2 1.0 C4B A:HEM901 3.0 19.8 1.0 C1A A:HEM901 3.0 19.1 1.0 C1D A:HEM901 3.0 22.9 1.0 C1C A:HEM901 3.0 21.2 1.0 C4C A:HEM901 3.1 23.1 1.0 C4A A:HEM901 3.1 18.5 1.0 C1B A:HEM901 3.2 17.6 1.0 C4 A:DTV2001 3.4 24.6 1.0 CHC A:HEM901 3.4 24.1 1.0 CHD A:HEM901 3.4 20.8 1.0 CHA A:HEM901 3.4 23.0 1.0 CHB A:HEM901 3.5 17.0 1.0 ND1 A:HIS20 4.1 23.7 1.0 CG A:HIS20 4.1 23.1 1.0 C2D A:HEM901 4.2 21.8 1.0 C3D A:HEM901 4.2 26.3 1.0 C2B A:HEM901 4.3 17.9 1.0 C3C A:HEM901 4.3 23.6 1.0 C3A A:HEM901 4.3 19.7 1.0 C2A A:HEM901 4.3 21.8 1.0 C2C A:HEM901 4.3 23.3 1.0 C3B A:HEM901 4.3 20.4 1.0 C3 A:DTV2001 4.5 31.6 1.0 CA A:GLY135 4.8 17.1 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt)


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 the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe902 b:17.9 occ:1.00 FE B:HEM902 0.0 17.9 1.0 NB B:HEM902 2.0 16.3 1.0 NA B:HEM902 2.0 16.1 1.0 ND B:HEM902 2.1 17.8 1.0 NE2 B:HIS320 2.1 17.3 1.0 NC B:HEM902 2.1 17.4 1.0 S4 B:DTV2002 2.3 18.4 1.0 C4D B:HEM902 3.0 18.5 1.0 C4B B:HEM902 3.0 17.0 1.0 CE1 B:HIS320 3.0 19.4 1.0 C1A B:HEM902 3.0 16.9 1.0 CD2 B:HIS320 3.0 17.4 1.0 C1C B:HEM902 3.1 18.6 1.0 C1B B:HEM902 3.1 17.7 1.0 C4A B:HEM902 3.1 17.2 1.0 C1D B:HEM902 3.1 20.8 1.0 C4C B:HEM902 3.2 19.2 1.0 C4 B:DTV2002 3.3 21.8 1.0 CHA B:HEM902 3.4 19.3 1.0 CHB B:HEM902 3.4 14.2 1.0 CHC B:HEM902 3.5 20.0 1.0 CHD B:HEM902 3.5 21.3 1.0 C3 B:DTV2002 4.1 19.8 1.0 ND1 B:HIS320 4.1 21.1 1.0 CG B:HIS320 4.2 19.0 1.0 C2B B:HEM902 4.2 16.8 1.0 C3B B:HEM902 4.2 21.9 1.0 C3D B:HEM902 4.2 22.7 1.0 C2D B:HEM902 4.2 22.9 1.0 C3A B:HEM902 4.3 18.0 1.0 C2C B:HEM902 4.3 22.0 1.0 C2A B:HEM902 4.3 17.9 1.0 C3C B:HEM902 4.3 22.9 1.0 CA B:GLY439 4.7 20.6 1.0 O B:HOH291 4.8 33.9 1.0 O3 B:DTV2002 4.8 21.9 1.0 CA B:GLY435 4.9 15.6 1.0 N B:GLY439 4.9 19.5 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Heme Oxygenase From Corynebacterium Diphtheriae (Hmuo) in Complex with Heme Binding Ditiothreitol (Dtt) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe903 b:23.9 occ:1.00 FE C:HEM903 0.0 23.9 1.0 NC C:HEM903 1.9 24.5 1.0 NB C:HEM903 2.0 21.7 1.0 NA C:HEM903 2.0 23.3 1.0 NE2 C:HIS620 2.0 23.2 1.0 ND C:HEM903 2.1 18.9 1.0 S4 C:DTV2003 2.3 27.1 1.0 C4B C:HEM903 3.0 21.6 1.0 CD2 C:HIS620 3.0 22.0 1.0 C4C C:HEM903 3.0 29.4 1.0 C4D C:HEM903 3.0 21.9 1.0 C1B C:HEM903 3.0 24.8 1.0 C1C C:HEM903 3.0 31.6 1.0 C4A C:HEM903 3.1 23.2 1.0 CE1 C:HIS620 3.1 27.3 1.0 C1A C:HEM903 3.1 23.1 1.0 C1D C:HEM903 3.1 25.7 1.0 C4 C:DTV2003 3.3 30.4 1.0 CHB C:HEM903 3.4 24.5 1.0 CHC C:HEM903 3.4 31.4 1.0 CHD C:HEM903 3.4 23.0 1.0 CHA C:HEM903 3.5 26.1 1.0 C2B C:HEM903 4.1 24.4 1.0 CG C:HIS620 4.2 24.4 1.0 ND1 C:HIS620 4.2 28.3 1.0 C3B C:HEM903 4.2 25.9 1.0 C3 C:DTV2003 4.2 28.9 1.0 C3A C:HEM903 4.2 22.1 1.0 C2D C:HEM903 4.2 26.4 1.0 C3C C:HEM903 4.3 29.1 1.0 C2C C:HEM903 4.3 31.8 1.0 C3D C:HEM903 4.3 28.7 1.0 C2A C:HEM903 4.3 23.1 1.0 CA C:GLY735 4.6 23.1 1.0 O3 C:DTV2003 5.0 29.2 1.0

T.Matsui, M.Iwasaki, R.Sugiyama, M.Unno, M.Ikeda-Saito. Dioxygen Activation For the Self-Degradation of Heme: Reaction Mechanism and Regulation of Heme Oxygenase. Inorg.Chem. V. 49 3602 2010.
ISSN: ISSN 0020-1669
PubMed: 20380462
DOI: 10.1021/IC901869T