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:
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
|