Iron in PDB 5wn8: Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1

All present enzymatic activity of Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1:
1.13.11.52;

The structure of Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1, PDB code: 5wn8 was solved by A.Lewis-Ballester, K.N.Pham, D.Batabyal, S.Karkashon, J.B.Bonanno, T.L.Poulos, S.R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.69 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.735, 97.785, 128.739, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.2

The structure of Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Iron atom in the Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 (pdb code 5wn8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1, PDB code: 5wn8:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:67.1 occ:1.00 FE A:HEM501 0.0 67.1 1.0 ND A:HEM501 1.9 70.4 1.0 NA A:HEM501 2.0 69.5 1.0 O12 A:BBJ502 2.1 0.5 1.0 NC A:HEM501 2.1 70.4 1.0 NB A:HEM501 2.1 69.6 1.0 NE2 A:HIS346 2.2 53.4 1.0 C4D A:HEM501 2.9 69.1 1.0 C1D A:HEM501 2.9 68.6 1.0 C1A A:HEM501 3.0 69.3 1.0 N11 A:BBJ502 3.0 0.0 1.0 CE1 A:HIS346 3.0 55.5 1.0 C4A A:HEM501 3.0 68.9 1.0 C4B A:HEM501 3.1 69.5 1.0 C1B A:HEM501 3.1 68.5 1.0 C4C A:HEM501 3.1 69.9 1.0 C1C A:HEM501 3.1 71.2 1.0 CD2 A:HIS346 3.2 54.3 1.0 CHA A:HEM501 3.4 69.6 1.0 CHD A:HEM501 3.4 68.0 1.0 CHB A:HEM501 3.4 68.1 1.0 CHC A:HEM501 3.5 69.8 1.0 C10 A:BBJ502 4.2 0.8 1.0 ND1 A:HIS346 4.2 53.9 1.0 C2D A:HEM501 4.2 67.7 1.0 C3D A:HEM501 4.2 67.5 1.0 C2A A:HEM501 4.2 72.1 1.0 C3A A:HEM501 4.2 70.8 1.0 C2C A:HEM501 4.3 73.8 1.0 C2B A:HEM501 4.3 69.3 1.0 CG A:HIS346 4.3 54.3 1.0 C3C A:HEM501 4.3 72.3 1.0 C3B A:HEM501 4.3 70.1 1.0 CB A:ALA264 4.4 80.3 1.0 N9 A:BBJ502 4.4 0.0 1.0

Iron binding site 2 out of 2 in the Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:70.3 occ:1.00 FE B:HEM501 0.0 70.3 1.0 ND B:HEM501 1.9 70.8 1.0 NA B:HEM501 2.0 71.1 1.0 O12 B:BBJ502 2.1 0.9 1.0 NC B:HEM501 2.1 67.0 1.0 NB B:HEM501 2.1 69.5 1.0 NE2 B:HIS346 2.2 69.3 1.0 C1D B:HEM501 2.9 69.5 1.0 C4D B:HEM501 2.9 71.3 1.0 C1A B:HEM501 3.0 73.3 1.0 N11 B:BBJ502 3.0 1.0 1.0 C4A B:HEM501 3.0 72.2 1.0 C1B B:HEM501 3.1 69.8 1.0 C4C B:HEM501 3.1 68.8 1.0 C4B B:HEM501 3.1 69.5 1.0 C1C B:HEM501 3.1 67.6 1.0 CE1 B:HIS346 3.2 69.6 1.0 CD2 B:HIS346 3.2 69.3 1.0 CHD B:HEM501 3.4 68.5 1.0 CHA B:HEM501 3.4 72.8 1.0 CHB B:HEM501 3.4 71.1 1.0 CHC B:HEM501 3.5 68.0 1.0 C10 B:BBJ502 4.2 0.3 1.0 C3D B:HEM501 4.2 70.9 1.0 C2D B:HEM501 4.2 70.4 1.0 C3A B:HEM501 4.2 75.4 1.0 C2A B:HEM501 4.2 76.3 1.0 ND1 B:HIS346 4.3 69.2 1.0 C3C B:HEM501 4.3 69.0 1.0 C2B B:HEM501 4.3 70.1 1.0 C2C B:HEM501 4.3 66.9 1.0 CB B:ALA264 4.3 72.3 1.0 C3B B:HEM501 4.3 70.0 1.0 CG B:HIS346 4.3 70.1 1.0 N9 B:BBJ502 4.4 0.0 1.0 N B:ALA264 4.9 77.0 1.0

A.Lewis-Ballester, K.N.Pham, D.Batabyal, S.Karkashon, J.B.Bonanno, T.L.Poulos, S.R.Yeh. Structural Insights Into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1. Nat Commun V. 8 1693 2017.
ISSN: ESSN 2041-1723
PubMed: 29167421
DOI: 10.1038/S41467-017-01725-8