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
|