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Iron in PDB 7a62: Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop

Enzymatic activity of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop

All present enzymatic activity of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop:
1.13.11.52;

Protein crystallography data

The structure of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop, PDB code: 7a62 was solved by M.Mirgaux, J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 2.44
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.960, 117.950, 216.410, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.7

Other elements in 7a62:

The structure of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop (pdb code 7a62). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop, PDB code: 7a62:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7a62

Go back to Iron Binding Sites List in 7a62
Iron binding site 1 out of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:41.2
occ:1.00
 FE A:HEM502 0.0 41.2 1.0
NB A:HEM502 1.9 38.8 1.0
NC A:HEM502 2.0 40.2 1.0
NA A:HEM502 2.0 42.9 1.0
ND A:HEM502 2.0 42.5 1.0
NE2 A:HIS346 2.3 33.6 1.0
C1B A:HEM502 2.9 36.8 1.0
C4A A:HEM502 3.0 43.6 1.0
C4C A:HEM502 3.0 40.9 1.0
C4B A:HEM502 3.0 34.8 1.0
C1C A:HEM502 3.0 39.2 1.0
C1D A:HEM502 3.0 38.8 1.0
C1A A:HEM502 3.1 45.0 1.0
C4D A:HEM502 3.1 41.2 1.0
CD2 A:HIS346 3.2 35.0 1.0
CB A:ALA264 3.3 45.5 1.0
CHB A:HEM502 3.3 40.6 1.0
CE1 A:HIS346 3.3 36.2 1.0
CHD A:HEM502 3.4 39.9 1.0
CHC A:HEM502 3.4 34.4 1.0
CHA A:HEM502 3.5 39.9 1.0
C A:ALA264 4.1 48.2 1.0
C2B A:HEM502 4.1 35.1 1.0
N A:GLY265 4.2 42.5 1.0
C3B A:HEM502 4.2 34.0 1.0
C3C A:HEM502 4.2 39.3 1.0
C2C A:HEM502 4.2 36.4 1.0
C3A A:HEM502 4.2 48.2 1.0
C2A A:HEM502 4.2 50.9 1.0
CA A:ALA264 4.2 46.9 1.0
C2D A:HEM502 4.3 37.8 1.0
C3D A:HEM502 4.3 39.0 1.0
CG A:HIS346 4.4 34.6 1.0
ND1 A:HIS346 4.4 37.9 1.0
O A:ALA264 4.5 43.8 1.0
CA A:GLY265 4.7 37.7 1.0
N A:ALA264 4.8 51.6 1.0
O A:HOH719 5.0 42.1 1.0

Iron binding site 2 out of 4 in 7a62

Go back to Iron Binding Sites List in 7a62
Iron binding site 2 out of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe503

b:39.5
occ:1.00
 FE B:HEM503 0.0 39.5 1.0
NC B:HEM503 1.9 42.4 1.0
NA B:HEM503 2.0 45.5 1.0
NB B:HEM503 2.0 40.9 1.0
ND B:HEM503 2.0 42.3 1.0
NE2 B:HIS346 2.3 37.4 1.0
C4C B:HEM503 2.9 42.8 1.0
C1C B:HEM503 3.0 39.9 1.0
C4A B:HEM503 3.0 44.9 1.0
C1B B:HEM503 3.0 41.1 1.0
C1A B:HEM503 3.0 46.6 1.0
C4B B:HEM503 3.0 33.9 1.0
C1D B:HEM503 3.0 44.1 1.0
C4D B:HEM503 3.0 44.9 1.0
CD2 B:HIS346 3.2 38.8 1.0
CHB B:HEM503 3.3 44.4 1.0
CHD B:HEM503 3.4 43.4 1.0
CB B:ALA264 3.4 42.9 1.0
CE1 B:HIS346 3.4 38.5 1.0
CHC B:HEM503 3.4 36.9 1.0
CHA B:HEM503 3.4 43.7 1.0
C B:ALA264 4.1 46.5 1.0
N B:GLY265 4.1 42.1 1.0
C3C B:HEM503 4.2 41.0 1.0
C2C B:HEM503 4.2 38.9 1.0
C3A B:HEM503 4.2 51.1 1.0
O B:HOH644 4.2 41.2 1.0
C2A B:HEM503 4.2 52.8 1.0
C2B B:HEM503 4.2 34.6 1.0
C3B B:HEM503 4.2 33.8 1.0
C2D B:HEM503 4.3 43.1 1.0
CA B:ALA264 4.3 44.5 1.0
C3D B:HEM503 4.3 45.5 1.0
CG B:HIS346 4.4 40.3 1.0
ND1 B:HIS346 4.5 41.3 1.0
O B:ALA264 4.6 42.1 1.0
CA B:GLY265 4.6 44.9 1.0
N B:ALA264 4.8 46.5 1.0

Iron binding site 3 out of 4 in 7a62

Go back to Iron Binding Sites List in 7a62
Iron binding site 3 out of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe504

b:53.4
occ:1.00
 FE C:HEM504 0.0 53.4 1.0
NB C:HEM504 1.9 46.8 1.0
NA C:HEM504 2.0 55.5 1.0
NC C:HEM504 2.1 47.8 1.0
ND C:HEM504 2.1 51.0 1.0
NE2 C:HIS346 2.4 49.8 1.0
C4A C:HEM504 2.9 53.0 1.0
C1B C:HEM504 2.9 47.2 1.0
C1A C:HEM504 2.9 58.0 1.0
C4B C:HEM504 3.0 42.4 1.0
C4C C:HEM504 3.1 49.5 1.0
C4D C:HEM504 3.1 51.2 1.0
C1C C:HEM504 3.1 40.3 1.0
C1D C:HEM504 3.1 53.0 1.0
CHB C:HEM504 3.2 48.5 1.0
CD2 C:HIS346 3.3 48.2 1.0
CE1 C:HIS346 3.3 54.8 1.0
CHA C:HEM504 3.4 56.0 1.0
CHC C:HEM504 3.4 39.6 1.0
CHD C:HEM504 3.5 51.2 1.0
CB C:ALA264 3.6 47.8 1.0
O C:HOH654 3.8 50.0 1.0
N C:GLY265 3.9 47.4 1.0
C C:ALA264 3.9 47.7 1.0
C3A C:HEM504 4.0 60.0 1.0
C2A C:HEM504 4.1 63.0 1.0
C2B C:HEM504 4.1 47.4 1.0
C3B C:HEM504 4.2 45.9 1.0
C3C C:HEM504 4.3 44.8 1.0
CA C:GLY265 4.3 47.1 1.0
CA C:ALA264 4.3 48.2 1.0
C2C C:HEM504 4.3 41.3 1.0
C3D C:HEM504 4.3 51.0 1.0
O C:ALA264 4.3 46.8 1.0
C2D C:HEM504 4.3 51.2 1.0
ND1 C:HIS346 4.4 56.6 1.0
CG C:HIS346 4.4 50.1 1.0
N C:ALA264 4.8 47.7 1.0

Iron binding site 4 out of 4 in 7a62

Go back to Iron Binding Sites List in 7a62
Iron binding site 4 out of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with A Complete Jk Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe504

b:53.4
occ:1.00
 FE D:HEM504 0.0 53.4 1.0
NB D:HEM504 1.9 48.4 1.0
NA D:HEM504 2.0 52.9 1.0
NC D:HEM504 2.1 49.0 1.0
ND D:HEM504 2.1 54.0 1.0
NE2 D:HIS346 2.4 50.0 1.0
C4A D:HEM504 2.9 55.4 1.0
C1B D:HEM504 2.9 47.3 1.0
C1A D:HEM504 3.0 59.9 1.0
C4B D:HEM504 3.0 44.5 1.0
C1C D:HEM504 3.1 45.6 1.0
C4D D:HEM504 3.1 52.0 1.0
C4C D:HEM504 3.1 47.2 1.0
C1D D:HEM504 3.1 52.4 1.0
CD2 D:HIS346 3.1 49.8 1.0
CHB D:HEM504 3.3 52.4 1.0
CHA D:HEM504 3.4 58.4 1.0
CHC D:HEM504 3.4 41.1 1.0
CE1 D:HIS346 3.4 51.8 1.0
CB D:ALA264 3.5 49.8 1.0
CHD D:HEM504 3.5 48.3 1.0
C D:ALA264 4.0 49.0 1.0
O D:HOH644 4.0 49.4 1.0
N D:GLY265 4.0 48.6 1.0
C3A D:HEM504 4.1 59.6 1.0
C2A D:HEM504 4.1 61.7 1.0
C2B D:HEM504 4.1 45.1 1.0
C3B D:HEM504 4.2 45.8 1.0
O D:ALA264 4.3 46.1 1.0
CA D:ALA264 4.3 50.5 1.0
C3D D:HEM504 4.3 50.7 1.0
C2C D:HEM504 4.3 43.0 1.0
C3C D:HEM504 4.3 41.2 1.0
C2D D:HEM504 4.3 49.8 1.0
CG D:HIS346 4.3 48.9 1.0
ND1 D:HIS346 4.4 52.1 1.0
CA D:GLY265 4.5 48.2 1.0
N D:ALA264 4.8 48.1 1.0

Reference:

M.Mirgaux, L.Leherte, J.Wouters. Influence of the Presence of the Heme Cofactor on the Jk-Loop Structure in Indoleamine 2,3-Dioxygenase 1. Acta Crystallogr D Struct V. 76 1211 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 33263327
DOI: 10.1107/S2059798320013510
Page generated: Wed Aug 7 21:46:33 2024

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