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Iron in PDB 7p0n: Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Open Conformation

Enzymatic activity of Crystal Structure of L-Trp/Indoleamine 2,3-Dioxygenagse 1 (HIDO1) Complex with the Jk-Loop Refined in the Open 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 Open 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 Open Conformation, PDB code: 7p0n 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) 49.29 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.36, 114.57, 220.98, 90, 90, 90
R / Rfree (%) 21.5 / 27.9

Other elements in 7p0n:

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

Chlorine (Cl) 2 atoms

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 Open Conformation (pdb code 7p0n). 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 Open Conformation, PDB code: 7p0n:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7p0n

Go back to Iron Binding Sites List in 7p0n
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 Open 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 Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:68.4
occ:1.00
FE A:HEM501 0.0 68.4 1.0
NA A:HEM501 2.0 68.4 1.0
ND A:HEM501 2.0 65.1 1.0
NB A:HEM501 2.1 65.2 1.0
NC A:HEM501 2.1 60.4 1.0
NE2 A:HIS346 2.5 62.1 1.0
O2 A:OXY510 3.0 75.1 1.0
C1A A:HEM501 3.0 70.7 1.0
C4A A:HEM501 3.0 70.5 1.0
C4D A:HEM501 3.0 67.0 1.0
C1B A:HEM501 3.1 65.3 1.0
C1D A:HEM501 3.1 64.7 1.0
C4B A:HEM501 3.1 57.6 1.0
C1C A:HEM501 3.1 58.5 1.0
C4C A:HEM501 3.2 58.4 1.0
CHA A:HEM501 3.4 65.2 1.0
CD2 A:HIS346 3.4 59.0 1.0
CE1 A:HIS346 3.4 63.8 1.0
CHB A:HEM501 3.4 69.7 1.0
CHD A:HEM501 3.5 61.8 1.0
CHC A:HEM501 3.5 56.4 1.0
CB A:ALA264 3.5 65.6 1.0
O1 A:OXY510 4.0 74.1 1.0
C2A A:HEM501 4.2 77.5 1.0
C3A A:HEM501 4.2 76.5 1.0
C3D A:HEM501 4.3 66.8 1.0
C2D A:HEM501 4.3 65.7 1.0
C2B A:HEM501 4.3 55.5 1.0
C3B A:HEM501 4.3 56.5 1.0
C A:ALA264 4.3 74.1 1.0
C2C A:HEM501 4.4 58.8 1.0
CA A:ALA264 4.4 76.7 1.0
N A:GLY265 4.4 70.4 1.0
C3C A:HEM501 4.4 53.8 1.0
ND1 A:HIS346 4.5 61.4 1.0
CG A:HIS346 4.6 58.2 1.0
N A:ALA264 4.7 82.9 1.0
O A:ALA264 4.8 72.9 1.0

Iron binding site 2 out of 4 in 7p0n

Go back to Iron Binding Sites List in 7p0n
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 Open 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 Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:71.3
occ:1.00
FE B:HEM501 0.0 71.3 1.0
NB B:HEM501 2.0 66.7 1.0
NC B:HEM501 2.0 59.3 1.0
NA B:HEM501 2.1 71.0 1.0
ND B:HEM501 2.2 68.3 1.0
NE2 B:HIS346 2.5 60.2 1.0
C1B B:HEM501 3.0 67.5 1.0
C4B B:HEM501 3.0 59.5 1.0
C4C B:HEM501 3.0 64.0 1.0
C4A B:HEM501 3.0 69.8 1.0
C1C B:HEM501 3.0 59.0 1.0
C1A B:HEM501 3.1 70.5 1.0
C1D B:HEM501 3.1 67.1 1.0
CB B:ALA264 3.2 70.4 1.0
C4D B:HEM501 3.2 67.4 1.0
CD2 B:HIS346 3.3 61.5 1.0
CHB B:HEM501 3.3 65.7 1.0
CHC B:HEM501 3.4 61.8 1.0
CHD B:HEM501 3.4 64.5 1.0
CHA B:HEM501 3.6 68.0 1.0
CE1 B:HIS346 3.6 66.5 1.0
C B:ALA264 3.8 68.4 1.0
N B:GLY265 3.9 71.8 1.0
O B:ALA264 4.1 63.3 1.0
CA B:ALA264 4.1 71.9 1.0
C2B B:HEM501 4.2 61.5 1.0
C3B B:HEM501 4.2 62.9 1.0
C3C B:HEM501 4.2 64.1 1.0
C2C B:HEM501 4.2 62.7 1.0
C3A B:HEM501 4.2 72.3 1.0
C2A B:HEM501 4.3 76.5 1.0
CA B:GLY265 4.4 64.7 1.0
C2D B:HEM501 4.4 70.6 1.0
C3D B:HEM501 4.4 71.0 1.0
CG B:HIS346 4.5 57.7 1.0
ND1 B:HIS346 4.6 69.9 1.0
N B:ALA264 4.9 72.5 1.0

Iron binding site 3 out of 4 in 7p0n

Go back to Iron Binding Sites List in 7p0n
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 Open 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 Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:63.5
occ:1.00
FE C:HEM501 0.0 63.5 1.0
NB C:HEM501 2.0 63.3 1.0
NC C:HEM501 2.1 58.4 1.0
NA C:HEM501 2.1 68.8 1.0
ND C:HEM501 2.1 65.9 1.0
NE2 C:HIS346 2.3 57.6 1.0
C1B C:HEM501 2.9 64.9 1.0
CB C:ALA264 2.9 62.4 1.0
C4A C:HEM501 3.0 70.5 1.0
C4C C:HEM501 3.0 59.7 1.0
C1D C:HEM501 3.1 64.5 1.0
C4B C:HEM501 3.1 53.6 1.0
C1C C:HEM501 3.1 55.6 1.0
C4D C:HEM501 3.2 68.6 1.0
CD2 C:HIS346 3.2 56.4 1.0
C1A C:HEM501 3.2 67.4 1.0
CHB C:HEM501 3.3 66.9 1.0
CE1 C:HIS346 3.4 58.4 1.0
CHD C:HEM501 3.4 60.4 1.0
CHC C:HEM501 3.5 54.0 1.0
CHA C:HEM501 3.6 65.5 1.0
CA C:ALA264 4.1 72.9 1.0
C C:ALA264 4.2 72.5 1.0
C2B C:HEM501 4.2 58.0 1.0
C3B C:HEM501 4.2 57.7 1.0
C3C C:HEM501 4.3 55.3 1.0
C3A C:HEM501 4.3 74.5 1.0
C2D C:HEM501 4.3 68.4 1.0
C2C C:HEM501 4.3 53.2 1.0
C3D C:HEM501 4.4 67.2 1.0
C2A C:HEM501 4.4 70.6 1.0
CG C:HIS346 4.4 59.7 1.0
N C:GLY265 4.4 67.0 1.0
ND1 C:HIS346 4.4 60.7 1.0
O C:ALA264 4.6 68.9 1.0
CA C:GLY265 5.0 69.5 1.0

Iron binding site 4 out of 4 in 7p0n

Go back to Iron Binding Sites List in 7p0n
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 Open 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 Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:68.4
occ:1.00
FE D:HEM501 0.0 68.4 1.0
NB D:HEM501 2.0 69.4 1.0
NA D:HEM501 2.1 73.4 1.0
NC D:HEM501 2.1 62.6 1.0
ND D:HEM501 2.1 68.5 1.0
NE2 D:HIS346 2.3 63.3 1.0
CE1 D:HIS346 2.8 62.5 1.0
C1B D:HEM501 3.0 68.3 1.0
C4A D:HEM501 3.0 71.0 1.0
C4C D:HEM501 3.1 67.5 1.0
C1A D:HEM501 3.1 72.1 1.0
C1D D:HEM501 3.1 66.4 1.0
C4B D:HEM501 3.1 61.7 1.0
C1C D:HEM501 3.2 57.2 1.0
C4D D:HEM501 3.2 65.3 1.0
CHB D:HEM501 3.3 64.9 1.0
CHD D:HEM501 3.4 66.8 1.0
CHC D:HEM501 3.5 61.0 1.0
CHA D:HEM501 3.5 66.3 1.0
CB D:ALA264 3.5 70.7 1.0
CD2 D:HIS346 3.6 66.9 1.0
O D:HOH612 3.7 62.0 1.0
ND1 D:HIS346 4.1 66.1 1.0
C D:ALA264 4.1 73.4 1.0
C3A D:HEM501 4.2 76.4 1.0
C2B D:HEM501 4.2 60.5 1.0
C2A D:HEM501 4.2 78.8 1.0
C3B D:HEM501 4.3 60.4 1.0
N D:GLY265 4.3 74.6 1.0
C3C D:HEM501 4.3 60.3 1.0
CA D:ALA264 4.3 73.7 1.0
C2C D:HEM501 4.3 58.8 1.0
C2D D:HEM501 4.3 65.3 1.0
C3D D:HEM501 4.4 63.8 1.0
CG D:HIS346 4.5 64.4 1.0
O D:ALA264 4.5 68.0 1.0
CA D:GLY265 4.7 65.1 1.0
N D:ALA264 4.8 73.6 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 14:51:07 2024

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