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Iron in PDB 6e40: Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat

Enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat

All present enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40 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) 46.86 / 2.31
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.367, 200.144, 114.741, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.4

Other elements in 6e40:

The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Bromine (Br) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat (pdb code 6e40). 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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6e40

Go back to Iron Binding Sites List in 6e40
Iron binding site 1 out of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:52.4
occ:1.00
FE A:HEM501 0.0 52.4 1.0
O12 A:BBJ502 1.8 61.1 1.0
NA A:HEM501 2.0 51.1 1.0
NE2 A:HIS346 2.0 56.0 1.0
NC A:HEM501 2.1 56.2 1.0
ND A:HEM501 2.1 60.4 1.0
NB A:HEM501 2.1 54.7 1.0
CE1 A:HIS346 2.7 51.8 1.0
N11 A:BBJ502 2.7 68.4 1.0
C4A A:HEM501 3.0 57.6 1.0
C4C A:HEM501 3.0 57.8 1.0
C1A A:HEM501 3.0 60.4 1.0
C1D A:HEM501 3.0 56.1 1.0
C4D A:HEM501 3.1 56.5 1.0
C1B A:HEM501 3.1 56.3 1.0
C1C A:HEM501 3.1 54.3 1.0
C4B A:HEM501 3.2 51.8 1.0
CD2 A:HIS346 3.2 55.1 1.0
CHD A:HEM501 3.4 58.5 1.0
CHB A:HEM501 3.4 57.0 1.0
CHA A:HEM501 3.4 55.1 1.0
CHC A:HEM501 3.5 52.1 1.0
C10 A:BBJ502 3.6 67.3 1.0
N9 A:BBJ502 3.9 64.5 1.0
ND1 A:HIS346 4.0 50.5 1.0
CG A:HIS346 4.2 54.5 1.0
C3A A:HEM501 4.2 60.2 1.0
C2A A:HEM501 4.2 60.9 1.0
C3C A:HEM501 4.3 55.8 1.0
C2D A:HEM501 4.3 54.1 1.0
C3D A:HEM501 4.3 53.5 1.0
C2C A:HEM501 4.3 53.2 1.0
C2B A:HEM501 4.3 57.4 1.0
C3B A:HEM501 4.4 55.9 1.0
CB A:ALA264 4.5 60.7 1.0
N A:ALA264 4.6 68.4 1.0
C13 A:BBJ502 4.9 68.7 1.0
CA A:ALA264 4.9 63.5 1.0

Iron binding site 2 out of 4 in 6e40

Go back to Iron Binding Sites List in 6e40
Iron binding site 2 out of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:51.7
occ:1.00
FE B:HEM501 0.0 51.7 1.0
O12 B:BBJ502 1.8 57.6 1.0
NE2 B:HIS346 2.0 51.3 1.0
NA B:HEM501 2.0 55.9 1.0
ND B:HEM501 2.0 50.5 1.0
NC B:HEM501 2.0 50.6 1.0
NB B:HEM501 2.0 54.2 1.0
CE1 B:HIS346 2.7 49.3 1.0
N11 B:BBJ502 2.8 62.2 1.0
C4A B:HEM501 3.0 56.6 1.0
C4D B:HEM501 3.0 53.6 1.0
C1A B:HEM501 3.0 57.0 1.0
C1D B:HEM501 3.0 52.2 1.0
C1B B:HEM501 3.1 53.3 1.0
C1C B:HEM501 3.1 54.5 1.0
C4C B:HEM501 3.1 52.9 1.0
C4B B:HEM501 3.1 52.8 1.0
CD2 B:HIS346 3.1 49.4 1.0
CHA B:HEM501 3.4 52.4 1.0
CHB B:HEM501 3.4 54.0 1.0
CHD B:HEM501 3.4 52.7 1.0
CHC B:HEM501 3.4 55.3 1.0
C10 B:BBJ502 3.6 60.1 1.0
N9 B:BBJ502 3.8 58.7 1.0
ND1 B:HIS346 3.9 51.2 1.0
CG B:HIS346 4.1 47.2 1.0
C3A B:HEM501 4.2 57.0 1.0
C3D B:HEM501 4.2 48.7 1.0
C2A B:HEM501 4.2 60.1 1.0
C2D B:HEM501 4.2 50.3 1.0
C2B B:HEM501 4.3 58.5 1.0
C3B B:HEM501 4.3 55.7 1.0
C3C B:HEM501 4.3 54.0 1.0
C2C B:HEM501 4.3 55.7 1.0
CB B:ALA264 4.4 55.6 1.0
N B:ALA264 4.9 55.4 1.0

Iron binding site 3 out of 4 in 6e40

Go back to Iron Binding Sites List in 6e40
Iron binding site 3 out of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:59.1
occ:1.00
FE C:HEM501 0.0 59.1 1.0
NA C:HEM501 2.0 58.2 1.0
ND C:HEM501 2.0 66.5 1.0
NC C:HEM501 2.1 61.5 1.0
NE2 C:HIS346 2.1 64.0 1.0
NB C:HEM501 2.2 58.8 1.0
CE1 C:HIS346 2.9 63.6 1.0
C4A C:HEM501 3.0 62.7 1.0
C4C C:HEM501 3.0 62.3 1.0
C1D C:HEM501 3.0 61.5 1.0
C1A C:HEM501 3.0 66.3 1.0
C4D C:HEM501 3.1 62.3 1.0
C1C C:HEM501 3.1 61.7 1.0
C1B C:HEM501 3.1 62.8 1.0
C4B C:HEM501 3.2 56.1 1.0
CD2 C:HIS346 3.3 63.6 1.0
CHD C:HEM501 3.4 64.1 1.0
CHB C:HEM501 3.4 61.6 1.0
CHA C:HEM501 3.4 64.5 1.0
CHC C:HEM501 3.5 56.6 1.0
N C:ALA264 4.1 66.8 1.0
ND1 C:HIS346 4.1 59.9 1.0
CB C:ALA264 4.2 61.2 1.0
C3A C:HEM501 4.2 65.4 1.0
C2A C:HEM501 4.2 64.5 1.0
C2D C:HEM501 4.3 62.4 1.0
C3C C:HEM501 4.3 61.7 1.0
C3D C:HEM501 4.3 62.7 1.0
C2C C:HEM501 4.3 61.6 1.0
CG C:HIS346 4.3 62.6 1.0
C2B C:HEM501 4.4 65.4 1.0
C3B C:HEM501 4.4 61.1 1.0
CA C:ALA264 4.6 64.6 1.0
N C:GLY265 4.8 66.5 1.0
C C:ALA264 4.9 69.2 1.0

Iron binding site 4 out of 4 in 6e40

Go back to Iron Binding Sites List in 6e40
Iron binding site 4 out of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat


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 the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:47.8
occ:1.00
FE D:HEM501 0.0 47.8 1.0
O12 D:BBJ502 1.8 55.8 1.0
NA D:HEM501 2.0 49.0 1.0
NB D:HEM501 2.0 49.4 1.0
ND D:HEM501 2.0 47.6 1.0
NC D:HEM501 2.1 48.0 1.0
NE2 D:HIS346 2.1 49.9 1.0
N11 D:BBJ502 2.7 56.6 1.0
CE1 D:HIS346 2.9 47.4 1.0
C4A D:HEM501 3.0 52.5 1.0
C1A D:HEM501 3.0 51.8 1.0
C1B D:HEM501 3.0 50.6 1.0
C4D D:HEM501 3.0 48.2 1.0
C1D D:HEM501 3.1 50.6 1.0
C4C D:HEM501 3.1 47.2 1.0
C4B D:HEM501 3.1 51.2 1.0
C1C D:HEM501 3.1 49.9 1.0
CD2 D:HIS346 3.1 50.1 1.0
CHB D:HEM501 3.4 51.0 1.0
CHA D:HEM501 3.4 49.0 1.0
CHD D:HEM501 3.4 50.0 1.0
CHC D:HEM501 3.5 50.2 1.0
C10 D:BBJ502 3.6 53.8 1.0
N9 D:BBJ502 4.0 52.1 1.0
ND1 D:HIS346 4.1 48.9 1.0
CG D:HIS346 4.2 49.5 1.0
C3A D:HEM501 4.2 55.4 1.0
C2A D:HEM501 4.2 54.7 1.0
C2B D:HEM501 4.3 51.6 1.0
C3D D:HEM501 4.3 45.9 1.0
C2D D:HEM501 4.3 48.5 1.0
C3B D:HEM501 4.3 49.6 1.0
C3C D:HEM501 4.3 53.3 1.0
C2C D:HEM501 4.3 51.4 1.0
CB D:ALA264 4.4 54.4 1.0
N D:ALA264 4.7 52.8 1.0
C13 D:BBJ502 4.9 57.8 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 17:13:29 2024

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