Iron in PDB 2d0u: Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase

All present enzymatic activity of Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase:
1.13.11.42;

The structure of Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase, PDB code: 2d0u was solved by H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, Y.Shiro, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.352, 97.089, 129.378, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.4

The binding sites of Iron atom in the Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase (pdb code 2d0u). 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 Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase, PDB code: 2d0u:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase


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 Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:22.6 occ:1.00 FE A:HEM404 0.0 22.6 1.0 ND A:HEM404 1.9 23.4 1.0 NE2 A:HIS346 2.0 18.1 1.0 C A:CYN405 2.0 31.2 1.0 NA A:HEM404 2.0 24.2 1.0 NB A:HEM404 2.1 23.0 1.0 NC A:HEM404 2.2 30.4 1.0 CE1 A:HIS346 2.8 14.1 1.0 C4D A:HEM404 3.0 23.6 1.0 C1D A:HEM404 3.0 25.4 1.0 C1A A:HEM404 3.0 25.7 1.0 CD2 A:HIS346 3.0 16.8 1.0 C4A A:HEM404 3.1 27.9 1.0 C1B A:HEM404 3.1 31.4 1.0 C4C A:HEM404 3.1 32.2 1.0 C4B A:HEM404 3.2 25.7 1.0 C1C A:HEM404 3.2 33.8 1.0 N A:CYN405 3.2 37.7 1.0 CHA A:HEM404 3.3 21.9 1.0 CHD A:HEM404 3.4 27.7 1.0 CHB A:HEM404 3.5 29.5 1.0 CHC A:HEM404 3.6 27.2 1.0 ND1 A:HIS346 4.0 16.5 1.0 CG A:HIS346 4.1 15.5 1.0 C2D A:HEM404 4.2 25.7 1.0 C3D A:HEM404 4.2 22.4 1.0 C2A A:HEM404 4.3 25.7 1.0 CB A:ALA264 4.3 51.5 1.0 C3A A:HEM404 4.3 26.2 1.0 C2B A:HEM404 4.3 35.3 1.0 C3B A:HEM404 4.4 31.5 1.0 C3C A:HEM404 4.4 38.0 1.0 C2C A:HEM404 4.4 40.0 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase


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 Cyanide Bound Form of Human Indoleamine 2,3- Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:17.9 occ:1.00 FE B:HEM404 0.0 17.9 1.0 ND B:HEM404 1.9 32.5 1.0 NE2 B:HIS346 2.0 21.0 1.0 C B:CYN1405 2.0 31.9 1.0 NA B:HEM404 2.1 21.1 1.0 NB B:HEM404 2.1 20.9 1.0 NC B:HEM404 2.1 27.8 1.0 CE1 B:HIS346 2.8 21.9 1.0 C4D B:HEM404 2.9 32.4 1.0 C1D B:HEM404 3.0 35.5 1.0 C1A B:HEM404 3.0 24.4 1.0 CD2 B:HIS346 3.1 19.2 1.0 C4A B:HEM404 3.1 25.4 1.0 C4C B:HEM404 3.1 30.1 1.0 C1B B:HEM404 3.2 24.7 1.0 C1C B:HEM404 3.2 26.6 1.0 N B:CYN1405 3.2 38.5 1.0 C4B B:HEM404 3.2 23.2 1.0 CHA B:HEM404 3.4 27.1 1.0 CHD B:HEM404 3.4 31.5 1.0 CHB B:HEM404 3.5 24.2 1.0 CHC B:HEM404 3.6 23.1 1.0 ND1 B:HIS346 4.0 22.3 1.0 C2D B:HEM404 4.2 36.6 1.0 CG B:HIS346 4.2 22.9 1.0 C3D B:HEM404 4.2 34.8 1.0 CB B:ALA264 4.2 50.8 1.0 C2A B:HEM404 4.3 26.4 1.0 C3A B:HEM404 4.3 26.0 1.0 C2B B:HEM404 4.4 23.7 1.0 C3C B:HEM404 4.4 29.9 1.0 C2C B:HEM404 4.4 29.4 1.0 C3B B:HEM404 4.4 22.5 1.0

H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, Y.Shiro. Crystal Structure of Human Indoleamine 2,3-Dioxygenase: Catalytic Mechanism of O2 Incorporation By A Heme-Containing Dioxygenase. Proc.Natl.Acad.Sci.Usa V. 103 2611 2006.
ISSN: ISSN 0027-8424
PubMed: 16477023
DOI: 10.1073/PNAS.0508996103