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Iron in PDB 6e42: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole, PDB code: 6e42 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) 49.07 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.742, 197.878, 113.019, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24

Other elements in 6e42:

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole (pdb code 6e42). 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 Ferric Heme and 4-Chlorophenyl Imidazole, PDB code: 6e42:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6e42

Go back to Iron Binding Sites List in 6e42
Iron binding site 1 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole


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 Ferric Heme and 4-Chlorophenyl Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:34.4
occ:1.00
 FE A:HEM501 0.0 34.4 1.0
NA A:HEM501 2.0 35.2 1.0
NC A:HEM501 2.0 34.8 1.0
ND A:HEM501 2.0 34.2 1.0
NB A:HEM501 2.1 34.9 1.0
NAJ A:HQJ502 2.1 33.8 1.0
NE2 A:HIS346 2.1 34.9 1.0
C4C A:HEM501 2.9 37.1 1.0
CE1 A:HIS346 2.9 34.1 1.0
C4A A:HEM501 3.0 39.4 1.0
C1A A:HEM501 3.0 38.9 1.0
C1B A:HEM501 3.0 33.4 1.0
CAK A:HQJ502 3.0 35.7 1.0
C1D A:HEM501 3.0 34.7 1.0
CAI A:HQJ502 3.0 33.4 1.0
C1C A:HEM501 3.1 35.1 1.0
C4D A:HEM501 3.1 35.8 1.0
CD2 A:HIS346 3.1 32.0 1.0
C4B A:HEM501 3.1 35.7 1.0
CHB A:HEM501 3.3 34.0 1.0
CHD A:HEM501 3.3 32.4 1.0
CHA A:HEM501 3.4 35.3 1.0
CHC A:HEM501 3.5 34.8 1.0
ND1 A:HIS346 4.1 37.0 1.0
CAH A:HQJ502 4.1 36.5 1.0
C3C A:HEM501 4.2 35.4 1.0
NAL A:HQJ502 4.2 37.7 1.0
C3A A:HEM501 4.2 37.8 1.0
CG A:HIS346 4.2 36.4 1.0
C2A A:HEM501 4.2 38.9 1.0
C2C A:HEM501 4.2 33.1 1.0
C2B A:HEM501 4.3 37.0 1.0
C2D A:HEM501 4.3 34.0 1.0
C3D A:HEM501 4.3 38.8 1.0
C3B A:HEM501 4.3 34.5 1.0
CB A:ALA264 4.7 32.7 1.0

Iron binding site 2 out of 4 in 6e42

Go back to Iron Binding Sites List in 6e42
Iron binding site 2 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole


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 Ferric Heme and 4-Chlorophenyl Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:31.9
occ:1.00
 FE B:HEM501 0.0 31.9 1.0
NA B:HEM501 1.9 36.4 1.0
NAJ B:HQJ502 2.0 28.8 1.0
NE2 B:HIS346 2.0 33.2 1.0
NC B:HEM501 2.0 32.0 1.0
NB B:HEM501 2.0 36.4 1.0
ND B:HEM501 2.1 30.9 1.0
CAK B:HQJ502 2.9 30.6 1.0
CE1 B:HIS346 2.9 32.3 1.0
C4A B:HEM501 2.9 38.9 1.0
C1A B:HEM501 3.0 37.1 1.0
C1B B:HEM501 3.0 34.3 1.0
C4D B:HEM501 3.0 33.9 1.0
C4C B:HEM501 3.1 32.9 1.0
CAI B:HQJ502 3.1 31.9 1.0
CD2 B:HIS346 3.1 33.2 1.0
C1C B:HEM501 3.1 38.9 1.0
C1D B:HEM501 3.1 31.5 1.0
C4B B:HEM501 3.1 36.1 1.0
CHB B:HEM501 3.4 33.0 1.0
CHA B:HEM501 3.4 35.1 1.0
CHD B:HEM501 3.4 31.2 1.0
CHC B:HEM501 3.5 34.9 1.0
ND1 B:HIS346 4.0 30.7 1.0
NAL B:HQJ502 4.0 32.1 1.0
CAH B:HQJ502 4.1 34.9 1.0
CG B:HIS346 4.1 30.2 1.0
C3A B:HEM501 4.1 40.1 1.0
C2A B:HEM501 4.2 39.3 1.0
C2B B:HEM501 4.3 40.1 1.0
C3C B:HEM501 4.3 33.5 1.0
C3D B:HEM501 4.3 34.0 1.0
C2C B:HEM501 4.3 36.6 1.0
C2D B:HEM501 4.3 34.8 1.0
C3B B:HEM501 4.3 36.4 1.0
CB B:ALA264 4.6 28.4 1.0

Iron binding site 3 out of 4 in 6e42

Go back to Iron Binding Sites List in 6e42
Iron binding site 3 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole


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 Ferric Heme and 4-Chlorophenyl Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:38.2
occ:1.00
 FE C:HEM501 0.0 38.2 1.0
NC C:HEM501 1.9 38.2 1.0
NA C:HEM501 2.0 34.2 1.0
NAJ C:HQJ502 2.0 37.9 1.0
NE2 C:HIS346 2.0 38.4 1.0
ND C:HEM501 2.1 39.6 1.0
NB C:HEM501 2.1 39.1 1.0
C4C C:HEM501 2.9 39.5 1.0
CE1 C:HIS346 3.0 39.7 1.0
C1C C:HEM501 3.0 38.4 1.0
CAI C:HQJ502 3.0 39.4 1.0
CAK C:HQJ502 3.0 40.4 1.0
CD2 C:HIS346 3.0 38.9 1.0
C4A C:HEM501 3.0 43.2 1.0
C1D C:HEM501 3.0 35.0 1.0
C1A C:HEM501 3.0 41.0 1.0
C4D C:HEM501 3.1 34.8 1.0
C1B C:HEM501 3.1 41.5 1.0
C4B C:HEM501 3.1 39.7 1.0
CHD C:HEM501 3.3 36.2 1.0
CHB C:HEM501 3.4 39.0 1.0
CHA C:HEM501 3.4 37.2 1.0
CHC C:HEM501 3.5 38.2 1.0
ND1 C:HIS346 4.1 41.7 1.0
C3C C:HEM501 4.1 40.9 1.0
CG C:HIS346 4.1 41.0 1.0
CAH C:HQJ502 4.1 37.3 1.0
NAL C:HQJ502 4.1 39.1 1.0
C2C C:HEM501 4.2 40.1 1.0
C3A C:HEM501 4.2 38.4 1.0
C2A C:HEM501 4.2 38.0 1.0
C2D C:HEM501 4.3 37.8 1.0
C3D C:HEM501 4.3 39.3 1.0
C2B C:HEM501 4.3 40.4 1.0
C3B C:HEM501 4.4 39.9 1.0
CB C:ALA264 4.6 34.1 1.0

Iron binding site 4 out of 4 in 6e42

Go back to Iron Binding Sites List in 6e42
Iron binding site 4 out of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complex with Ferric Heme and 4-Chlorophenyl Imidazole


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 Ferric Heme and 4-Chlorophenyl Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:33.7
occ:1.00
 FE D:HEM501 0.0 33.7 1.0
NE2 D:HIS346 2.0 35.5 1.0
NA D:HEM501 2.0 34.6 1.0
NC D:HEM501 2.0 33.1 1.0
NB D:HEM501 2.0 36.6 1.0
ND D:HEM501 2.0 33.3 1.0
NAJ D:HQJ502 2.0 33.7 1.0
CE1 D:HIS346 2.8 33.1 1.0
CAK D:HQJ502 2.9 33.4 1.0
C4A D:HEM501 3.0 36.0 1.0
C4C D:HEM501 3.0 31.7 1.0
C1B D:HEM501 3.0 35.7 1.0
C1D D:HEM501 3.0 31.7 1.0
C4D D:HEM501 3.1 31.6 1.0
C1A D:HEM501 3.1 35.7 1.0
CD2 D:HIS346 3.1 35.1 1.0
C1C D:HEM501 3.1 35.8 1.0
C4B D:HEM501 3.1 35.9 1.0
CAI D:HQJ502 3.1 33.2 1.0
CHB D:HEM501 3.3 31.7 1.0
CHD D:HEM501 3.3 30.7 1.0
CHA D:HEM501 3.5 36.5 1.0
CHC D:HEM501 3.5 31.1 1.0
ND1 D:HIS346 4.0 34.9 1.0
NAL D:HQJ502 4.1 34.7 1.0
CG D:HIS346 4.1 33.6 1.0
CAH D:HQJ502 4.2 32.7 1.0
C3A D:HEM501 4.2 36.3 1.0
C3C D:HEM501 4.2 32.7 1.0
C2B D:HEM501 4.2 37.0 1.0
C2D D:HEM501 4.3 35.3 1.0
C2A D:HEM501 4.3 38.1 1.0
C3D D:HEM501 4.3 38.7 1.0
C2C D:HEM501 4.3 34.4 1.0
C3B D:HEM501 4.3 34.2 1.0
CB D:ALA264 4.6 30.4 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 17:13:45 2024

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