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Iron in PDB 7p0r: Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation

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

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

Protein crystallography data

The structure of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation, PDB code: 7p0r 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) 49.22 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.89, 115.72, 217.53, 90, 90, 90
R / Rfree (%) 21.8 / 28.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation (pdb code 7p0r). 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-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation, PDB code: 7p0r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7p0r

Go back to Iron Binding Sites List in 7p0r
Iron binding site 1 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate 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-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:68.7
occ:1.00
 FE A:HEM501 0.0 68.7 1.0
NB A:HEM501 2.0 64.6 1.0
NA A:HEM501 2.0 68.5 1.0
NC A:HEM501 2.1 65.3 1.0
ND A:HEM501 2.2 68.7 1.0
NE2 A:HIS346 2.4 61.3 1.0
C1B A:HEM501 3.0 63.1 1.0
C4A A:HEM501 3.0 69.5 1.0
C4B A:HEM501 3.1 56.0 1.0
C1A A:HEM501 3.1 73.2 1.0
C4C A:HEM501 3.1 63.6 1.0
C1C A:HEM501 3.2 61.9 1.0
C1D A:HEM501 3.2 65.2 1.0
C4D A:HEM501 3.2 70.5 1.0
CD2 A:HIS346 3.3 59.2 1.0
CHB A:HEM501 3.3 67.5 1.0
CE1 A:HIS346 3.4 63.6 1.0
CHC A:HEM501 3.5 55.1 1.0
CHD A:HEM501 3.5 65.4 1.0
CHA A:HEM501 3.5 69.4 1.0
CB A:ALA264 3.6 60.4 1.0
C2B A:HEM501 4.2 59.8 1.0
C3A A:HEM501 4.2 76.3 1.0
C3B A:HEM501 4.2 58.9 1.0
N A:GLY265 4.2 68.3 1.0
C2A A:HEM501 4.3 80.1 1.0
C3C A:HEM501 4.3 59.4 1.0
C2C A:HEM501 4.4 59.8 1.0
C A:ALA264 4.4 71.9 1.0
CG A:HIS346 4.4 60.7 1.0
C3D A:HEM501 4.4 70.0 1.0
C2D A:HEM501 4.4 69.7 1.0
CA A:ALA264 4.5 69.6 1.0
ND1 A:HIS346 4.5 67.5 1.0
N A:ALA264 4.8 74.6 1.0
CA A:GLY265 4.9 63.1 1.0

Iron binding site 2 out of 4 in 7p0r

Go back to Iron Binding Sites List in 7p0r
Iron binding site 2 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate 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-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:79.8
occ:1.00
 FE B:HEM501 0.0 79.8 1.0
NA B:HEM501 2.0 76.7 1.0
NB B:HEM501 2.0 74.1 1.0
NC B:HEM501 2.1 76.5 1.0
ND B:HEM501 2.2 80.2 1.0
NE2 B:HIS346 2.4 71.8 1.0
C1B B:HEM501 3.0 70.8 1.0
C4A B:HEM501 3.0 77.9 1.0
C4B B:HEM501 3.0 62.3 1.0
C1A B:HEM501 3.0 79.5 1.0
C1C B:HEM501 3.1 64.9 1.0
CD2 B:HIS346 3.1 71.4 1.0
C4C B:HEM501 3.1 74.5 1.0
C4D B:HEM501 3.2 76.6 1.0
C1D B:HEM501 3.2 78.4 1.0
CHB B:HEM501 3.4 73.4 1.0
CHC B:HEM501 3.4 59.7 1.0
CHA B:HEM501 3.5 77.3 1.0
CHD B:HEM501 3.5 74.3 1.0
CE1 B:HIS346 3.6 72.4 1.0
CB B:ALA264 3.7 72.1 1.0
N B:GLY265 4.0 75.7 1.0
C B:ALA264 4.1 73.3 1.0
C2B B:HEM501 4.2 65.0 1.0
C3B B:HEM501 4.2 61.3 1.0
C3A B:HEM501 4.2 85.3 1.0
C2A B:HEM501 4.2 85.7 1.0
C2C B:HEM501 4.3 62.9 1.0
CA B:ALA264 4.3 76.4 1.0
C3C B:HEM501 4.4 67.6 1.0
CG B:HIS346 4.4 69.3 1.0
C3D B:HEM501 4.4 74.5 1.0
C2D B:HEM501 4.4 74.8 1.0
ND1 B:HIS346 4.5 74.3 1.0
CA B:GLY265 4.6 66.8 1.0
O B:ALA264 4.6 71.4 1.0
N B:ALA264 4.6 75.3 1.0

Iron binding site 3 out of 4 in 7p0r

Go back to Iron Binding Sites List in 7p0r
Iron binding site 3 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate 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-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:65.7
occ:1.00
 FE C:HEM501 0.0 65.7 1.0
NA C:HEM501 2.0 64.6 1.0
ND C:HEM501 2.1 66.2 1.0
NC C:HEM501 2.1 66.1 1.0
NB C:HEM501 2.1 65.1 1.0
NE2 C:HIS346 2.4 62.7 1.0
C4A C:HEM501 3.0 68.7 1.0
C1A C:HEM501 3.0 69.5 1.0
C1B C:HEM501 3.1 61.8 1.0
C4C C:HEM501 3.1 65.9 1.0
C4D C:HEM501 3.1 63.9 1.0
C1D C:HEM501 3.1 65.4 1.0
CD2 C:HIS346 3.1 61.0 1.0
C1C C:HEM501 3.2 59.8 1.0
C4B C:HEM501 3.2 56.0 1.0
CB C:ALA264 3.3 63.2 1.0
CHB C:HEM501 3.3 64.5 1.0
CHA C:HEM501 3.4 63.5 1.0
CHD C:HEM501 3.4 63.7 1.0
CE1 C:HIS346 3.5 61.8 1.0
CHC C:HEM501 3.6 56.5 1.0
C3A C:HEM501 4.2 71.8 1.0
C2A C:HEM501 4.2 75.0 1.0
N C:GLY265 4.2 66.9 1.0
C C:ALA264 4.2 72.2 1.0
CA C:ALA264 4.2 66.1 1.0
C2B C:HEM501 4.3 61.1 1.0
C3C C:HEM501 4.3 60.4 1.0
C2D C:HEM501 4.3 69.1 1.0
C3D C:HEM501 4.3 67.1 1.0
C2C C:HEM501 4.4 57.9 1.0
C3B C:HEM501 4.4 59.6 1.0
CG C:HIS346 4.4 61.4 1.0
ND1 C:HIS346 4.5 69.3 1.0
N C:ALA264 4.6 74.4 1.0
O C:ALA264 4.8 70.2 1.0
CA C:GLY265 4.9 62.9 1.0

Iron binding site 4 out of 4 in 7p0r

Go back to Iron Binding Sites List in 7p0r
Iron binding site 4 out of 4 in the Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate 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-Dioxygenase (HIDO1) Complex with the Jk-Loop Refined in the Intermediate Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:80.3
occ:1.00
 FE D:HEM501 0.0 80.3 1.0
NA D:HEM501 2.0 74.0 1.0
NB D:HEM501 2.0 73.9 1.0
ND D:HEM501 2.1 74.8 1.0
NC D:HEM501 2.1 73.8 1.0
NE2 D:HIS346 2.4 68.1 1.0
C1A D:HEM501 3.0 77.4 1.0
C4B D:HEM501 3.0 65.5 1.0
C4A D:HEM501 3.0 74.4 1.0
C1B D:HEM501 3.1 72.9 1.0
C4D D:HEM501 3.1 71.1 1.0
CD2 D:HIS346 3.1 69.8 1.0
C1C D:HEM501 3.1 66.0 1.0
C1D D:HEM501 3.2 74.0 1.0
C4C D:HEM501 3.2 70.5 1.0
CHA D:HEM501 3.4 72.0 1.0
CB D:ALA264 3.4 71.6 1.0
CHB D:HEM501 3.4 71.6 1.0
CHC D:HEM501 3.4 62.8 1.0
CE1 D:HIS346 3.6 68.3 1.0
CHD D:HEM501 3.6 70.0 1.0
N D:GLY265 4.0 76.7 1.0
C D:ALA264 4.1 73.8 1.0
CA D:ALA264 4.2 75.5 1.0
C2A D:HEM501 4.2 82.2 1.0
C3B D:HEM501 4.2 66.9 1.0
C3A D:HEM501 4.2 77.5 1.0
C2B D:HEM501 4.2 66.9 1.0
C3D D:HEM501 4.3 73.8 1.0
C2C D:HEM501 4.3 64.0 1.0
CG D:HIS346 4.3 65.2 1.0
C2D D:HEM501 4.4 70.6 1.0
C3C D:HEM501 4.4 66.9 1.0
CA D:GLY265 4.5 70.0 1.0
ND1 D:HIS346 4.5 73.7 1.0
N D:ALA264 4.6 74.3 1.0
O D:ALA264 4.6 69.0 1.0
CG2 D:VAL350 4.9 60.7 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 14:52:50 2024

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