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Iron in PDB 7nge: Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation

Enzymatic activity of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation

All present enzymatic activity of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation, PDB code: 7nge 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) 46.87 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.36, 114.67, 219.67, 90, 90, 90
R / Rfree (%) 21.5 / 27.1

Other elements in 7nge:

The structure of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation (pdb code 7nge). 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 L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation, PDB code: 7nge:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7nge

Go back to Iron Binding Sites List in 7nge
Iron binding site 1 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation


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 L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe511

b:57.9
occ:1.00
 FE A:HEM511 0.0 57.9 1.0
ND A:HEM511 1.9 62.9 1.0
NC A:HEM511 2.1 58.4 1.0
NA A:HEM511 2.1 59.5 1.0
NB A:HEM511 2.2 57.1 1.0
NE2 A:HIS346 2.3 54.4 1.0
C1D A:HEM511 2.9 62.0 1.0
C4D A:HEM511 3.0 64.9 1.0
C4C A:HEM511 3.0 56.8 1.0
CD2 A:HIS346 3.1 52.3 1.0
C1A A:HEM511 3.1 58.2 1.0
C1C A:HEM511 3.1 51.5 1.0
C4A A:HEM511 3.2 59.0 1.0
C1B A:HEM511 3.2 59.3 1.0
C4B A:HEM511 3.2 53.9 1.0
CHD A:HEM511 3.3 57.6 1.0
CHA A:HEM511 3.4 60.5 1.0
CE1 A:HIS346 3.5 56.8 1.0
CD1 A:TRP501 3.5 59.9 0.7
CHC A:HEM511 3.6 53.3 1.0
CHB A:HEM511 3.6 59.6 1.0
NE1 A:TRP501 3.8 63.6 0.7
C2D A:HEM511 4.1 63.6 1.0
C3D A:HEM511 4.2 65.4 1.0
C3C A:HEM511 4.2 53.0 1.0
CB A:ALA264 4.3 61.4 1.0
C2C A:HEM511 4.3 54.5 1.0
CG A:HIS346 4.3 49.8 1.0
C2A A:HEM511 4.3 63.0 1.0
C3A A:HEM511 4.4 60.6 1.0
C2B A:HEM511 4.4 55.0 1.0
C3B A:HEM511 4.5 50.8 1.0
ND1 A:HIS346 4.5 54.2 1.0
OG A:SER263 4.7 72.5 1.0
N A:ALA264 4.7 68.4 1.0
CG A:TRP501 4.8 60.2 0.7
O A:HOH665 4.9 58.9 1.0
CA A:ALA264 5.0 64.6 1.0

Iron binding site 2 out of 4 in 7nge

Go back to Iron Binding Sites List in 7nge
Iron binding site 2 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation


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 L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe511

b:56.9
occ:1.00
 FE B:HEM511 0.0 56.9 1.0
NB B:HEM511 2.0 57.2 1.0
NA B:HEM511 2.1 64.0 1.0
ND B:HEM511 2.1 58.7 1.0
NC B:HEM511 2.1 56.1 1.0
NE2 B:HIS346 2.3 49.7 1.0
C1B B:HEM511 3.0 58.1 1.0
C4A B:HEM511 3.0 61.3 1.0
C4B B:HEM511 3.1 54.5 1.0
CD2 B:HIS346 3.1 49.5 1.0
C1D B:HEM511 3.1 58.7 1.0
C4C B:HEM511 3.1 57.2 1.0
C1A B:HEM511 3.1 62.3 1.0
C4D B:HEM511 3.1 59.1 1.0
C1C B:HEM511 3.1 54.0 1.0
O B:HOH630 3.2 57.9 1.0
CHB B:HEM511 3.3 56.8 1.0
CE1 B:HIS346 3.4 54.2 1.0
CHD B:HEM511 3.4 56.9 1.0
CHC B:HEM511 3.5 53.2 1.0
CHA B:HEM511 3.5 59.2 1.0
C2B B:HEM511 4.2 55.5 1.0
CA B:ALA264 4.2 68.4 1.0
C3A B:HEM511 4.2 66.0 1.0
C3B B:HEM511 4.2 55.5 1.0
O B:ALA264 4.3 66.7 1.0
CG B:HIS346 4.3 47.9 1.0
C2A B:HEM511 4.3 65.8 1.0
C3C B:HEM511 4.3 51.6 1.0
C2D B:HEM511 4.3 61.8 1.0
C2C B:HEM511 4.4 48.9 1.0
C3D B:HEM511 4.4 62.2 1.0
ND1 B:HIS346 4.4 53.8 1.0
C B:ALA264 4.5 67.0 1.0
O B:HOH736 4.6 59.7 1.0
O B:HOH604 4.6 61.0 1.0
N B:ALA264 4.9 71.9 1.0
CG2 B:VAL350 5.0 45.9 1.0

Iron binding site 3 out of 4 in 7nge

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Iron binding site 3 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation


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 L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe514

b:58.6
occ:1.00
 FE C:HEM514 0.0 58.6 1.0
NC C:HEM514 2.0 60.5 1.0
ND C:HEM514 2.0 64.3 1.0
NB C:HEM514 2.1 56.5 1.0
NA C:HEM514 2.1 59.0 1.0
NE2 C:HIS346 2.4 57.4 1.0
C4C C:HEM514 2.9 59.7 1.0
C1D C:HEM514 3.0 62.6 1.0
C1C C:HEM514 3.1 54.2 1.0
C4D C:HEM514 3.1 62.1 1.0
C1B C:HEM514 3.1 57.8 1.0
C4B C:HEM514 3.1 51.8 1.0
C4A C:HEM514 3.1 57.3 1.0
CD2 C:HIS346 3.1 54.9 1.0
C1A C:HEM514 3.2 56.7 1.0
CB C:ALA264 3.3 63.4 1.0
CHD C:HEM514 3.3 60.0 1.0
CHC C:HEM514 3.5 52.5 1.0
CHB C:HEM514 3.5 59.6 1.0
CHA C:HEM514 3.5 58.0 1.0
CE1 C:HIS346 3.5 58.0 1.0
C C:ALA264 4.0 69.3 1.0
N C:GLY265 4.2 66.3 1.0
C3C C:HEM514 4.2 58.0 1.0
C2D C:HEM514 4.2 68.0 1.0
C2C C:HEM514 4.2 57.8 1.0
CA C:ALA264 4.3 67.8 1.0
C3D C:HEM514 4.3 66.7 1.0
O C:ALA264 4.3 63.4 1.0
C3B C:HEM514 4.3 51.9 1.0
C2B C:HEM514 4.3 58.8 1.0
CG C:HIS346 4.4 54.6 1.0
C3A C:HEM514 4.4 61.0 1.0
C2A C:HEM514 4.4 62.5 1.0
ND1 C:HIS346 4.5 58.6 1.0
CA C:GLY265 4.6 63.5 1.0

Iron binding site 4 out of 4 in 7nge

Go back to Iron Binding Sites List in 7nge
Iron binding site 4 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation


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 L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe507

b:62.3
occ:1.00
 FE D:HEM507 0.0 62.3 1.0
ND D:HEM507 2.0 66.9 1.0
NC D:HEM507 2.0 67.8 1.0
NB D:HEM507 2.1 61.5 1.0
NA D:HEM507 2.1 62.8 1.0
NE2 D:HIS346 2.4 57.3 1.0
C1D D:HEM507 3.0 67.8 1.0
C4C D:HEM507 3.0 61.2 1.0
C4D D:HEM507 3.0 67.9 1.0
C1C D:HEM507 3.1 58.1 1.0
C4B D:HEM507 3.1 55.3 1.0
C1A D:HEM507 3.1 59.6 1.0
C4A D:HEM507 3.2 60.8 1.0
C1B D:HEM507 3.2 61.7 1.0
CD2 D:HIS346 3.2 56.3 1.0
CHD D:HEM507 3.3 62.6 1.0
CE1 D:HIS346 3.4 59.4 1.0
CHA D:HEM507 3.4 59.0 1.0
CHC D:HEM507 3.5 54.9 1.0
CB D:ALA264 3.5 64.5 1.0
CHB D:HEM507 3.5 61.5 1.0
C D:ALA264 4.0 72.6 1.0
C2D D:HEM507 4.2 71.4 1.0
C3C D:HEM507 4.2 59.3 1.0
O D:ALA264 4.2 66.4 1.0
C3D D:HEM507 4.2 72.0 1.0
CA D:ALA264 4.2 68.3 1.0
C2C D:HEM507 4.2 59.4 1.0
C3B D:HEM507 4.3 52.5 1.0
N D:GLY265 4.3 73.8 1.0
C3A D:HEM507 4.4 62.1 1.0
C2A D:HEM507 4.4 64.3 1.0
C2B D:HEM507 4.4 59.4 1.0
CG D:HIS346 4.4 53.9 1.0
ND1 D:HIS346 4.5 60.3 1.0
CA D:GLY265 4.7 65.2 1.0

Reference:

M.Mirgaux, L.Leherte, J.Wouters. Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of An Exo Site International Journal of 2021TRYPTOPHAN Research.
DOI: 10.1177/11786469211052964
Page generated: Thu Aug 8 09:35:13 2024

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