Iron in PDB 3moo: Crystal Structure of the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme

The structure of Crystal Structure of the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme, PDB code: 3moo was solved by K.Omori, 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)	50.00 / 1.71
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.609, 63.649, 78.520, 90.00, 130.34, 90.00
R / Rfree (%)	17.8 / 21.3

The binding sites of Iron atom in the Crystal Structure of the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme (pdb code 3moo). 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 the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme, PDB code: 3moo:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme


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 Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe911 b:12.6 occ:1.00 FE A:VEA911 0.0 12.6 1.0 N1 A:VEA911 2.0 13.9 1.0 N2 A:VEA911 2.0 13.4 1.0 N4 A:VEA911 2.0 14.5 1.0 N3 A:VEA911 2.0 13.7 1.0 NE2 A:HIS20 2.1 12.2 1.0 N3 A:AZI217 2.2 13.5 1.0 C1B A:VEA911 2.8 13.9 1.0 N2 A:AZI217 2.9 17.1 1.0 C1A A:VEA911 2.9 14.3 1.0 C4D A:VEA911 3.0 14.0 1.0 C4A A:VEA911 3.0 14.2 1.0 C4C A:VEA911 3.0 13.9 1.0 CD2 A:HIS20 3.0 12.9 1.0 C1D A:VEA911 3.1 13.9 1.0 C1C A:VEA911 3.1 14.2 1.0 C4B A:VEA911 3.2 14.1 1.0 CE1 A:HIS20 3.2 12.6 1.0 CHB A:VEA911 3.2 14.6 1.0 CHA A:VEA911 3.3 13.9 1.0 CHD A:VEA911 3.4 13.9 1.0 O A:VEA911 3.6 14.8 1.0 N1 A:AZI217 3.7 17.8 1.0 C2A A:VEA911 4.2 13.9 1.0 C3A A:VEA911 4.2 14.3 1.0 C2B A:VEA911 4.2 13.9 1.0 CG A:HIS20 4.2 14.0 1.0 C3D A:VEA911 4.2 14.0 1.0 ND1 A:HIS20 4.3 13.5 1.0 C2D A:VEA911 4.3 13.9 1.0 C3C A:VEA911 4.3 13.6 1.0 C3B A:VEA911 4.3 14.4 1.0 C2C A:VEA911 4.4 13.8 1.0 N A:GLY139 4.4 11.1 1.0 CA A:GLY139 4.6 10.9 1.0 CA A:GLY135 4.8 9.2 1.0 CB A:SER138 4.8 10.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme


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 Hmuo, Heme Oxygenase From Corynebacterium Diphtheriae, in Complex with Azide-Bound Verdoheme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe912 b:13.1 occ:1.00 FE B:VEA912 0.0 13.1 1.0 N3 B:AZI217 1.9 10.7 1.0 N1 B:VEA912 2.0 13.8 1.0 N2 B:VEA912 2.0 14.3 1.0 N3 B:VEA912 2.0 14.1 1.0 N4 B:VEA912 2.0 14.0 1.0 NE2 B:HIS20 2.3 17.5 1.0 N2 B:AZI217 2.5 16.9 1.0 C4B B:VEA912 3.0 14.2 1.0 C1A B:VEA912 3.0 13.9 1.0 C4C B:VEA912 3.0 14.1 1.0 C1C B:VEA912 3.0 14.3 1.0 C4A B:VEA912 3.0 14.8 1.0 C1D B:VEA912 3.0 14.0 1.0 C4D B:VEA912 3.1 14.0 1.0 C1B B:VEA912 3.1 14.4 1.0 CD2 B:HIS20 3.1 17.0 1.0 O B:VEA912 3.3 13.9 1.0 CE1 B:HIS20 3.4 16.9 1.0 CHD B:VEA912 3.4 14.2 1.0 CHA B:VEA912 3.4 13.9 1.0 CHB B:VEA912 3.5 14.5 1.0 N1 B:AZI217 3.5 20.2 1.0 C3C B:VEA912 4.2 14.1 1.0 C3A B:VEA912 4.2 14.6 1.0 C3B B:VEA912 4.2 14.4 1.0 C2D B:VEA912 4.3 14.1 1.0 C2A B:VEA912 4.3 14.5 1.0 C3D B:VEA912 4.3 13.9 1.0 C2B B:VEA912 4.3 14.1 1.0 C2C B:VEA912 4.3 14.1 1.0 CG B:HIS20 4.3 15.6 1.0 N B:GLY139 4.3 12.3 1.0 ND1 B:HIS20 4.4 15.8 1.0 CA B:GLY135 4.6 10.2 1.0 CA B:GLY139 4.6 11.9 1.0 CB B:SER138 4.9 11.5 1.0 O B:GLY135 5.0 10.3 1.0

W.Lai, H.Chen, T.Matsui, K.Omori, M.Unno, M.Ikeda-Saito, S.Shaik. Enzymatic Ring-Opening Mechanism of Verdoheme By the Heme Oxygenase: A Combined X-Ray Crystallography and Qm/Mm Study. J.Am.Chem.Soc. V. 132 12960 2010.
ISSN: ISSN 0002-7863
PubMed: 20806922
DOI: 10.1021/JA104674Q