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Iron in PDB 6e45: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State, PDB code: 6e45 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) 65.88 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.969, 196.538, 116.207, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State (pdb code 6e45). 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) Free Enzyme in the Ferrous State, PDB code: 6e45:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6e45

Go back to Iron Binding Sites List in 6e45
Iron binding site 1 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State


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) Free Enzyme in the Ferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:33.1
occ:1.00
 FE A:HEM501 0.0 33.1 1.0
NA A:HEM501 2.0 30.7 1.0
NC A:HEM501 2.0 29.9 1.0
NB A:HEM501 2.1 28.6 1.0
ND A:HEM501 2.1 30.3 1.0
NE2 A:HIS346 2.2 35.0 1.0
C4A A:HEM501 3.0 32.3 1.0
C1B A:HEM501 3.0 29.3 1.0
C4C A:HEM501 3.0 31.1 1.0
C1A A:HEM501 3.1 34.1 1.0
C1D A:HEM501 3.1 29.6 1.0
C1C A:HEM501 3.1 29.8 1.0
C4B A:HEM501 3.1 28.3 1.0
CD2 A:HIS346 3.1 34.5 1.0
C4D A:HEM501 3.1 30.8 1.0
CE1 A:HIS346 3.2 37.7 1.0
CHB A:HEM501 3.4 29.4 1.0
CHD A:HEM501 3.4 31.1 1.0
CHA A:HEM501 3.5 31.9 1.0
CHC A:HEM501 3.5 29.4 1.0
CB A:ALA264 4.0 31.6 1.0
C3A A:HEM501 4.2 35.7 1.0
C2B A:HEM501 4.2 30.5 1.0
ND1 A:HIS346 4.3 33.4 1.0
C3C A:HEM501 4.3 29.1 1.0
C2A A:HEM501 4.3 33.4 1.0
O A:HOH756 4.3 36.5 1.0
CG A:HIS346 4.3 35.0 1.0
C3B A:HEM501 4.3 28.8 1.0
C2C A:HEM501 4.3 31.7 1.0
C2D A:HEM501 4.3 36.2 1.0
C3D A:HEM501 4.3 32.1 1.0
N A:GLY265 4.5 29.8 1.0
C A:ALA264 4.6 30.5 1.0
CA A:ALA264 4.8 32.1 1.0

Iron binding site 2 out of 4 in 6e45

Go back to Iron Binding Sites List in 6e45
Iron binding site 2 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State


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) Free Enzyme in the Ferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.7
occ:1.00
 FE B:HEM501 0.0 30.7 1.0
NA B:HEM501 2.0 32.2 1.0
NB B:HEM501 2.0 28.3 1.0
NC B:HEM501 2.0 32.4 1.0
ND B:HEM501 2.1 31.0 1.0
NE2 B:HIS346 2.2 30.8 1.0
C1B B:HEM501 3.0 29.4 1.0
C4A B:HEM501 3.0 34.4 1.0
C4C B:HEM501 3.0 33.4 1.0
C4B B:HEM501 3.1 31.1 1.0
C1A B:HEM501 3.1 33.7 1.0
C1C B:HEM501 3.1 27.9 1.0
C1D B:HEM501 3.1 32.6 1.0
C4D B:HEM501 3.1 30.5 1.0
CD2 B:HIS346 3.1 30.8 1.0
CE1 B:HIS346 3.2 31.1 1.0
CHB B:HEM501 3.3 28.7 1.0
CHD B:HEM501 3.4 32.1 1.0
CHC B:HEM501 3.5 29.9 1.0
CHA B:HEM501 3.5 31.6 1.0
CB B:ALA264 3.9 29.9 1.0
C2B B:HEM501 4.2 29.5 1.0
C3A B:HEM501 4.2 34.8 1.0
C3B B:HEM501 4.2 29.4 1.0
C3C B:HEM501 4.3 29.3 1.0
ND1 B:HIS346 4.3 30.1 1.0
C2A B:HEM501 4.3 36.2 1.0
C2C B:HEM501 4.3 32.8 1.0
CG B:HIS346 4.3 29.2 1.0
C2D B:HEM501 4.3 34.2 1.0
O B:HOH800 4.3 35.1 1.0
C3D B:HEM501 4.3 30.2 1.0
N B:GLY265 4.6 28.4 1.0
C B:ALA264 4.6 29.4 1.0
CA B:ALA264 4.8 28.5 1.0

Iron binding site 3 out of 4 in 6e45

Go back to Iron Binding Sites List in 6e45
Iron binding site 3 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State


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) Free Enzyme in the Ferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:28.9
occ:1.00
 FE C:HEM501 0.0 28.9 1.0
NC C:HEM501 2.0 25.5 1.0
NB C:HEM501 2.0 28.7 1.0
NA C:HEM501 2.1 29.6 1.0
NE2 C:HIS346 2.1 29.7 1.0
ND C:HEM501 2.1 29.2 1.0
C1B C:HEM501 3.0 28.0 1.0
CE1 C:HIS346 3.0 29.8 1.0
C4C C:HEM501 3.0 26.2 1.0
C4A C:HEM501 3.0 30.9 1.0
CD2 C:HIS346 3.1 26.5 1.0
C1C C:HEM501 3.1 26.2 1.0
C4B C:HEM501 3.1 27.1 1.0
C1D C:HEM501 3.1 28.8 1.0
C1A C:HEM501 3.1 33.1 1.0
C4D C:HEM501 3.1 29.1 1.0
CHB C:HEM501 3.4 30.7 1.0
CHD C:HEM501 3.4 28.3 1.0
CHC C:HEM501 3.5 25.1 1.0
CHA C:HEM501 3.5 31.0 1.0
CB C:ALA264 4.0 28.0 1.0
ND1 C:HIS346 4.1 28.3 1.0
CG C:HIS346 4.2 29.9 1.0
O C:HOH787 4.2 31.3 1.0
C2B C:HEM501 4.2 29.8 1.0
C3C C:HEM501 4.2 27.2 1.0
C3B C:HEM501 4.3 28.1 1.0
C2C C:HEM501 4.3 25.2 1.0
C3A C:HEM501 4.3 36.2 1.0
C2A C:HEM501 4.3 34.2 1.0
C2D C:HEM501 4.3 31.8 1.0
C3D C:HEM501 4.3 29.5 1.0
N C:GLY265 4.5 27.5 1.0
C C:ALA264 4.6 28.2 1.0
CA C:ALA264 4.8 29.4 1.0
CG2 C:VAL350 4.9 28.7 1.0

Iron binding site 4 out of 4 in 6e45

Go back to Iron Binding Sites List in 6e45
Iron binding site 4 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State


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) Free Enzyme in the Ferrous State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:27.4
occ:1.00
 FE D:HEM501 0.0 27.4 1.0
NB D:HEM501 2.0 26.5 1.0
NA D:HEM501 2.0 29.4 1.0
ND D:HEM501 2.0 29.6 1.0
NC D:HEM501 2.1 27.6 1.0
NE2 D:HIS346 2.2 25.6 1.0
C1B D:HEM501 3.0 25.7 1.0
C4A D:HEM501 3.0 30.7 1.0
C1D D:HEM501 3.1 27.0 1.0
CE1 D:HIS346 3.1 28.0 1.0
C4B D:HEM501 3.1 27.6 1.0
C4D D:HEM501 3.1 29.2 1.0
C4C D:HEM501 3.1 28.8 1.0
C1A D:HEM501 3.1 30.1 1.0
C1C D:HEM501 3.1 25.0 1.0
CD2 D:HIS346 3.2 28.9 1.0
CHB D:HEM501 3.4 26.8 1.0
CHD D:HEM501 3.4 28.6 1.0
CHA D:HEM501 3.4 30.8 1.0
CHC D:HEM501 3.5 25.5 1.0
O D:HOH765 4.0 33.0 1.0
CB D:ALA264 4.0 28.4 1.0
ND1 D:HIS346 4.2 25.4 1.0
C2B D:HEM501 4.2 26.9 1.0
C3B D:HEM501 4.3 26.0 1.0
CG D:HIS346 4.3 28.0 1.0
C3A D:HEM501 4.3 32.4 1.0
C2D D:HEM501 4.3 27.9 1.0
C3D D:HEM501 4.3 28.1 1.0
C2A D:HEM501 4.3 32.6 1.0
C3C D:HEM501 4.3 27.8 1.0
C2C D:HEM501 4.3 28.9 1.0
N D:GLY265 4.7 26.1 1.0
C D:ALA264 4.7 26.2 1.0
CA D:ALA264 4.8 26.9 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: Sun Dec 13 16:24:50 2020

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