Iron in PDB 2d0t: Crystal Structure of 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase

All present enzymatic activity of Crystal Structure of 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase:
1.13.11.42;

The structure of Crystal Structure of 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase, PDB code: 2d0t was solved by H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, Y.Shiro, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.070, 98.027, 130.951, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.1

The binding sites of Iron atom in the Crystal Structure of 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase (pdb code 2d0t). 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 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase, PDB code: 2d0t:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of 4-Phenylimidazole 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 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:34.5 occ:1.00 FE A:HEM404 0.0 34.5 1.0 NB A:HEM404 2.0 38.5 1.0 ND A:HEM404 2.0 37.1 1.0 NA A:HEM404 2.0 40.7 1.0 NE2 A:HIS346 2.1 29.0 1.0 N3 A:PIM501 2.1 31.0 1.0 NC A:HEM404 2.1 36.0 1.0 C1B A:HEM404 3.0 37.3 1.0 C4A A:HEM404 3.0 38.1 1.0 CE1 A:HIS346 3.0 37.6 1.0 C2 A:PIM501 3.0 39.2 1.0 C4D A:HEM404 3.0 40.8 1.0 C1A A:HEM404 3.0 39.9 1.0 C1D A:HEM404 3.0 37.5 1.0 C4 A:PIM501 3.1 34.8 1.0 C4B A:HEM404 3.1 40.4 1.0 CD2 A:HIS346 3.1 36.1 1.0 C4C A:HEM404 3.1 44.9 1.0 C1C A:HEM404 3.2 48.2 1.0 CHB A:HEM404 3.3 44.2 1.0 CHA A:HEM404 3.4 44.5 1.0 CHD A:HEM404 3.4 41.9 1.0 CHC A:HEM404 3.5 34.5 1.0 ND1 A:HIS346 4.1 36.3 1.0 N1 A:PIM501 4.2 36.0 1.0 CG A:HIS346 4.2 34.0 1.0 C5 A:PIM501 4.2 33.5 1.0 C3A A:HEM404 4.2 41.5 1.0 C2B A:HEM404 4.2 43.0 1.0 C2A A:HEM404 4.3 41.1 1.0 C2D A:HEM404 4.3 36.8 1.0 C3D A:HEM404 4.3 38.0 1.0 C3B A:HEM404 4.3 47.0 1.0 C2C A:HEM404 4.4 48.5 1.0 C3C A:HEM404 4.4 46.8 1.0 CB A:ALA264 4.7 39.5 1.0

Iron binding site 2 out of 2 in the Crystal Structure of 4-Phenylimidazole 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 4-Phenylimidazole Bound Form of Human Indoleamine 2,3-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:36.1 occ:1.00 FE B:HEM404 0.0 36.1 1.0 NB B:HEM404 2.0 33.0 1.0 ND B:HEM404 2.0 45.6 1.0 NA B:HEM404 2.1 35.7 1.0 NE2 B:HIS346 2.1 35.2 1.0 N3 B:PIM1501 2.1 40.7 1.0 NC B:HEM404 2.1 36.5 1.0 C2 B:PIM1501 3.0 47.4 1.0 C1B B:HEM404 3.0 37.4 1.0 C4A B:HEM404 3.0 37.6 1.0 C1D B:HEM404 3.0 43.2 1.0 CE1 B:HIS346 3.1 43.9 1.0 C4D B:HEM404 3.1 42.4 1.0 CD2 B:HIS346 3.1 32.5 1.0 C4C B:HEM404 3.1 42.5 1.0 C1A B:HEM404 3.1 45.9 1.0 C4B B:HEM404 3.1 39.2 1.0 C4 B:PIM1501 3.2 45.1 1.0 C1C B:HEM404 3.2 41.6 1.0 CHB B:HEM404 3.3 39.7 1.0 CHD B:HEM404 3.4 37.4 1.0 CHA B:HEM404 3.5 46.4 1.0 CHC B:HEM404 3.5 41.1 1.0 ND1 B:HIS346 4.2 37.3 1.0 N1 B:PIM1501 4.2 44.5 1.0 CG B:HIS346 4.2 34.2 1.0 C2B B:HEM404 4.2 41.4 1.0 C5 B:PIM1501 4.3 41.3 1.0 C3A B:HEM404 4.3 45.0 1.0 C2D B:HEM404 4.3 45.1 1.0 C3D B:HEM404 4.3 40.8 1.0 C2A B:HEM404 4.3 41.0 1.0 C3B B:HEM404 4.3 40.5 1.0 C3C B:HEM404 4.4 40.9 1.0 C2C B:HEM404 4.4 40.3 1.0 CB B:ALA264 4.7 32.2 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