Iron in PDB 5wmx: 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: 5wmx was solved by A.Lewis-Ballester, S.R.Yeh, K.N.Pham, D.Batabyal, S.Karkashon, J.B.Bonanno, T.M.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.10 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.057, 97.566, 130.416, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.4

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 5wmx). 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: 5wmx:
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:90.1 occ:1.00 FE A:HEM501 0.0 90.1 1.0 C A:CYN500 1.9 93.8 1.0 ND A:HEM501 1.9 89.1 1.0 NE2 A:HIS346 1.9 83.0 1.0 NA A:HEM501 2.0 91.8 1.0 NC A:HEM501 2.1 89.4 1.0 NB A:HEM501 2.1 91.9 1.0 CE1 A:HIS346 2.9 82.6 1.0 C4D A:HEM501 2.9 89.1 1.0 C1D A:HEM501 2.9 87.2 1.0 CD2 A:HIS346 3.0 80.8 1.0 N A:CYN500 3.0 97.1 1.0 C1A A:HEM501 3.0 91.8 1.0 C4A A:HEM501 3.0 93.5 1.0 C4B A:HEM501 3.1 92.1 1.0 C1B A:HEM501 3.1 93.5 1.0 C4C A:HEM501 3.1 87.8 1.0 C1C A:HEM501 3.1 90.5 1.0 CHA A:HEM501 3.4 90.8 1.0 CHD A:HEM501 3.4 87.0 1.0 CHB A:HEM501 3.4 94.3 1.0 CHC A:HEM501 3.5 91.5 1.0 ND1 A:HIS346 4.0 81.4 1.0 CG A:HIS346 4.1 80.4 1.0 C3D A:HEM501 4.2 86.7 1.0 C2D A:HEM501 4.2 85.8 1.0 C2A A:HEM501 4.2 94.2 1.0 C3A A:HEM501 4.2 94.9 1.0 C2B A:HEM501 4.3 94.8 1.0 C3C A:HEM501 4.3 88.4 1.0 C2C A:HEM501 4.3 90.0 1.0 C3B A:HEM501 4.3 94.1 1.0 CD1 A:TRP502 4.5 0.4 1.0 CB A:ALA264 4.6 90.0 1.0 NE1 A:TRP502 4.7 0.7 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:0.1 occ:1.00 FE B:HEM501 0.0 0.1 1.0 C B:CYN500 1.9 0.6 1.0 ND B:HEM501 1.9 0.1 1.0 NE2 B:HIS346 1.9 97.6 1.0 NA B:HEM501 2.0 0.3 1.0 NC B:HEM501 2.1 0.9 1.0 NB B:HEM501 2.1 0.8 1.0 CE1 B:HIS346 2.9 98.2 1.0 C1D B:HEM501 2.9 0.7 1.0 C4D B:HEM501 2.9 0.6 1.0 CD2 B:HIS346 3.0 95.5 1.0 C1A B:HEM501 3.0 0.1 1.0 N B:CYN500 3.0 0.8 1.0 C4A B:HEM501 3.0 0.8 1.0 C4B B:HEM501 3.1 0.8 1.0 C1B B:HEM501 3.1 1.0 1.0 C4C B:HEM501 3.1 99.3 1.0 C1C B:HEM501 3.1 0.8 1.0 CHA B:HEM501 3.4 0.6 1.0 CHD B:HEM501 3.4 98.8 1.0 CHB B:HEM501 3.4 0.5 1.0 CHC B:HEM501 3.5 0.0 1.0 ND1 B:HIS346 4.0 98.4 1.0 CG B:HIS346 4.1 96.6 1.0 C2D B:HEM501 4.2 1.0 1.0 C3D B:HEM501 4.2 0.9 1.0 C2A B:HEM501 4.2 0.0 1.0 C3A B:HEM501 4.2 0.9 1.0 C2C B:HEM501 4.3 99.6 1.0 C2B B:HEM501 4.3 0.4 1.0 C3C B:HEM501 4.3 99.5 1.0 C3B B:HEM501 4.3 0.7 1.0 CB B:ALA264 4.5 92.1 1.0 CD1 B:TRP502 4.6 98.9 1.0 NE1 B:TRP502 4.7 96.6 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