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Iron in PDB 6e46: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan, PDB code: 6e46 was solved by S.Luo, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.30 / 2.09
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.916, 197.189, 115.016, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan (pdb code 6e46). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan, PDB code: 6e46:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6e46

Go back to Iron Binding Sites List in 6e46
Iron binding site 1 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan


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 Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:35.1
occ:1.00
 FE A:HEM501 0.0 35.1 1.0
NA A:HEM501 2.1 32.6 1.0
NB A:HEM501 2.1 33.7 1.0
NC A:HEM501 2.1 36.0 1.0
ND A:HEM501 2.1 33.6 1.0
NE2 A:HIS346 2.3 36.5 1.0
C1B A:HEM501 3.0 35.3 1.0
C4A A:HEM501 3.0 36.4 1.0
C4C A:HEM501 3.0 38.7 1.0
C1D A:HEM501 3.1 37.6 1.0
C4B A:HEM501 3.1 35.8 1.0
C1A A:HEM501 3.1 39.4 1.0
C1C A:HEM501 3.1 35.1 1.0
C4D A:HEM501 3.1 38.6 1.0
CD2 A:HIS346 3.2 33.5 1.0
CE1 A:HIS346 3.3 36.1 1.0
CHB A:HEM501 3.3 34.3 1.0
CHD A:HEM501 3.4 36.1 1.0
CHC A:HEM501 3.5 35.2 1.0
CHA A:HEM501 3.5 34.6 1.0
CD1 A:TRP502 4.0 42.0 1.0
NE1 A:TRP502 4.1 51.2 1.0
C2B A:HEM501 4.2 34.6 1.0
C3C A:HEM501 4.3 36.8 1.0
C3A A:HEM501 4.3 38.0 1.0
C3B A:HEM501 4.3 32.0 1.0
C2D A:HEM501 4.3 37.7 1.0
C2A A:HEM501 4.3 36.9 1.0
C2C A:HEM501 4.3 37.0 1.0
C3D A:HEM501 4.3 39.4 1.0
ND1 A:HIS346 4.3 36.2 1.0
CG A:HIS346 4.3 34.8 1.0
CB A:ALA264 4.4 47.1 1.0
N A:ALA264 4.9 47.5 1.0
CG1 A:VAL350 5.0 37.9 1.0

Iron binding site 2 out of 4 in 6e46

Go back to Iron Binding Sites List in 6e46
Iron binding site 2 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan


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 Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:32.4
occ:1.00
 FE B:HEM501 0.0 32.4 1.0
NA B:HEM501 2.0 32.5 1.0
NB B:HEM501 2.0 32.9 1.0
NC B:HEM501 2.1 35.1 1.0
ND B:HEM501 2.1 33.6 1.0
NE2 B:HIS346 2.2 32.3 1.0
C1B B:HEM501 3.0 33.5 1.0
C4A B:HEM501 3.0 35.4 1.0
C4C B:HEM501 3.1 37.7 1.0
C1A B:HEM501 3.1 35.3 1.0
C1D B:HEM501 3.1 36.4 1.0
C4D B:HEM501 3.1 35.4 1.0
C4B B:HEM501 3.1 35.9 1.0
C1C B:HEM501 3.1 36.6 1.0
CD2 B:HIS346 3.1 34.3 1.0
CE1 B:HIS346 3.3 32.8 1.0
CHB B:HEM501 3.3 32.9 1.0
CHD B:HEM501 3.4 35.6 1.0
CHA B:HEM501 3.5 31.9 1.0
CHC B:HEM501 3.5 33.6 1.0
CD1 B:TRP502 4.0 39.9 1.0
NE1 B:TRP502 4.2 41.9 1.0
C2B B:HEM501 4.2 35.2 1.0
C3A B:HEM501 4.2 37.9 1.0
C3B B:HEM501 4.3 35.0 1.0
CG B:HIS346 4.3 34.0 1.0
C2A B:HEM501 4.3 37.7 1.0
C2D B:HEM501 4.3 33.4 1.0
C3C B:HEM501 4.3 39.5 1.0
C2C B:HEM501 4.3 39.5 1.0
C3D B:HEM501 4.3 33.0 1.0
ND1 B:HIS346 4.3 35.3 1.0
CB B:ALA264 4.4 37.2 1.0
O B:HOH671 4.7 38.8 1.0
N B:ALA264 4.9 39.0 1.0

Iron binding site 3 out of 4 in 6e46

Go back to Iron Binding Sites List in 6e46
Iron binding site 3 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:39.7
occ:1.00
 FE C:HEM501 0.0 39.7 1.0
NC C:HEM501 2.0 43.2 1.0
NA C:HEM501 2.0 38.5 1.0
ND C:HEM501 2.1 42.7 1.0
NB C:HEM501 2.1 40.8 1.0
NE2 C:HIS346 2.3 44.7 1.0
C4C C:HEM501 3.0 42.2 1.0
C1D C:HEM501 3.0 42.6 1.0
C4A C:HEM501 3.0 43.6 1.0
C1B C:HEM501 3.1 42.6 1.0
C1C C:HEM501 3.1 43.0 1.0
C1A C:HEM501 3.1 46.1 1.0
C4D C:HEM501 3.1 41.3 1.0
C4B C:HEM501 3.1 41.6 1.0
CD2 C:HIS346 3.2 45.0 1.0
CE1 C:HIS346 3.3 43.8 1.0
CHD C:HEM501 3.4 41.7 1.0
CHB C:HEM501 3.4 42.5 1.0
CHC C:HEM501 3.5 42.8 1.0
CHA C:HEM501 3.5 45.0 1.0
CD1 C:TRP503 4.0 47.2 1.0
NE1 C:TRP503 4.1 51.1 1.0
CB C:ALA264 4.1 51.0 1.0
C3C C:HEM501 4.2 43.9 1.0
C2C C:HEM501 4.2 41.8 1.0
C2D C:HEM501 4.3 44.3 1.0
C3A C:HEM501 4.3 45.3 1.0
C2B C:HEM501 4.3 40.6 1.0
C2A C:HEM501 4.3 46.1 1.0
C3D C:HEM501 4.3 43.0 1.0
CG C:HIS346 4.3 45.3 1.0
C3B C:HEM501 4.3 39.6 1.0
ND1 C:HIS346 4.4 44.6 1.0
N C:ALA264 4.8 54.6 1.0
CA C:ALA264 5.0 43.8 1.0

Iron binding site 4 out of 4 in 6e46

Go back to Iron Binding Sites List in 6e46
Iron binding site 4 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferrous Heme and Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:38.9
occ:1.00
 FE D:HEM501 0.0 38.9 1.0
NB D:HEM501 2.0 37.4 1.0
NA D:HEM501 2.0 38.1 1.0
ND D:HEM501 2.0 37.1 1.0
NC D:HEM501 2.1 38.0 1.0
NE2 D:HIS346 2.3 37.4 1.0
C1B D:HEM501 3.0 37.2 1.0
C4A D:HEM501 3.0 39.4 1.0
C1D D:HEM501 3.0 42.4 1.0
C4C D:HEM501 3.0 38.0 1.0
C4B D:HEM501 3.1 39.9 1.0
C4D D:HEM501 3.1 39.0 1.0
C1A D:HEM501 3.1 40.5 1.0
C1C D:HEM501 3.1 34.0 1.0
CD2 D:HIS346 3.2 40.3 1.0
CE1 D:HIS346 3.3 39.3 1.0
CHB D:HEM501 3.3 35.7 1.0
CHD D:HEM501 3.3 38.1 1.0
CHA D:HEM501 3.5 37.7 1.0
CHC D:HEM501 3.5 36.7 1.0
CD1 D:TRP503 3.8 41.6 1.0
NE1 D:TRP503 4.0 47.0 1.0
C2B D:HEM501 4.2 36.4 1.0
C3A D:HEM501 4.2 42.8 1.0
C2D D:HEM501 4.3 42.5 1.0
C3B D:HEM501 4.3 35.1 1.0
C3C D:HEM501 4.3 39.9 1.0
C3D D:HEM501 4.3 38.6 1.0
C2A D:HEM501 4.3 43.4 1.0
CG D:HIS346 4.3 36.3 1.0
C2C D:HEM501 4.3 37.0 1.0
ND1 D:HIS346 4.3 39.8 1.0
CB D:ALA264 4.4 47.8 1.0
N D:ALA264 4.8 46.0 1.0
O D:HOH623 4.8 45.2 1.0

Reference:

S.Luo, K.Xu, S.Xiang, J.Chen, C.Chen, C.Guo, Y.Tong, L.Tong. High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Tue Aug 6 17:18:15 2024

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