Iron in PDB 6tue: Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
Enzymatic activity of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
All present enzymatic activity of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop:
1.13.11.52;
Protein crystallography data
The structure of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop, PDB code: 6tue
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)
|
49.19 /
2.61
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.960,
117.950,
216.470,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
27.7
|
Other elements in 6tue:
The structure of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
(pdb code 6tue). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop, PDB code: 6tue:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6tue
Go back to
Iron Binding Sites List in 6tue
Iron binding site 1 out
of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:52.0
occ:1.00
|
FE
|
A:HEM502
|
0.0
|
52.0
|
1.0
|
NB
|
A:HEM502
|
2.0
|
48.9
|
1.0
|
NA
|
A:HEM502
|
2.0
|
52.1
|
1.0
|
NC
|
A:HEM502
|
2.0
|
48.6
|
1.0
|
ND
|
A:HEM502
|
2.1
|
50.5
|
1.0
|
NE2
|
A:HIS346
|
2.5
|
44.0
|
1.0
|
C4A
|
A:HEM502
|
2.9
|
52.2
|
1.0
|
C1B
|
A:HEM502
|
2.9
|
47.2
|
1.0
|
C4C
|
A:HEM502
|
3.0
|
48.4
|
1.0
|
C1A
|
A:HEM502
|
3.0
|
53.8
|
1.0
|
C1C
|
A:HEM502
|
3.0
|
45.6
|
1.0
|
C4B
|
A:HEM502
|
3.0
|
44.0
|
1.0
|
C1D
|
A:HEM502
|
3.1
|
48.1
|
1.0
|
C4D
|
A:HEM502
|
3.1
|
49.9
|
1.0
|
CHB
|
A:HEM502
|
3.3
|
51.8
|
1.0
|
CB
|
A:ALA264
|
3.3
|
46.4
|
1.0
|
CD2
|
A:HIS346
|
3.4
|
44.3
|
1.0
|
CHD
|
A:HEM502
|
3.4
|
47.8
|
1.0
|
CHC
|
A:HEM502
|
3.4
|
42.6
|
1.0
|
CHA
|
A:HEM502
|
3.5
|
51.6
|
1.0
|
CE1
|
A:HIS346
|
3.5
|
44.3
|
1.0
|
C
|
A:ALA264
|
4.0
|
54.4
|
1.0
|
C3A
|
A:HEM502
|
4.1
|
56.0
|
1.0
|
C2A
|
A:HEM502
|
4.2
|
57.3
|
1.0
|
N
|
A:GLY265
|
4.2
|
48.9
|
1.0
|
C2B
|
A:HEM502
|
4.2
|
41.8
|
1.0
|
C2C
|
A:HEM502
|
4.2
|
44.2
|
1.0
|
CA
|
A:ALA264
|
4.2
|
51.3
|
1.0
|
C3C
|
A:HEM502
|
4.2
|
48.5
|
1.0
|
C3B
|
A:HEM502
|
4.2
|
41.9
|
1.0
|
C2D
|
A:HEM502
|
4.3
|
47.6
|
1.0
|
C3D
|
A:HEM502
|
4.3
|
47.5
|
1.0
|
O
|
A:HOH635
|
4.3
|
40.9
|
1.0
|
O
|
A:ALA264
|
4.5
|
50.2
|
1.0
|
CG
|
A:HIS346
|
4.6
|
43.3
|
1.0
|
ND1
|
A:HIS346
|
4.6
|
45.4
|
1.0
|
CA
|
A:GLY265
|
4.7
|
48.2
|
1.0
|
N
|
A:ALA264
|
4.7
|
58.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 6tue
Go back to
Iron Binding Sites List in 6tue
Iron binding site 2 out
of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe503
b:53.8
occ:1.00
|
FE
|
B:HEM503
|
0.0
|
53.8
|
1.0
|
NA
|
B:HEM503
|
1.9
|
58.4
|
1.0
|
NB
|
B:HEM503
|
1.9
|
53.6
|
1.0
|
NC
|
B:HEM503
|
2.0
|
54.9
|
1.0
|
ND
|
B:HEM503
|
2.1
|
57.1
|
1.0
|
NE2
|
B:HIS346
|
2.4
|
54.4
|
1.0
|
C4A
|
B:HEM503
|
2.9
|
60.6
|
1.0
|
C1B
|
B:HEM503
|
2.9
|
51.8
|
1.0
|
C4C
|
B:HEM503
|
3.0
|
53.4
|
1.0
|
C4B
|
B:HEM503
|
3.0
|
48.1
|
1.0
|
C1A
|
B:HEM503
|
3.0
|
60.2
|
1.0
|
C1C
|
B:HEM503
|
3.0
|
54.0
|
1.0
|
C1D
|
B:HEM503
|
3.0
|
54.8
|
1.0
|
CB
|
B:ALA264
|
3.1
|
47.0
|
1.0
|
C4D
|
B:HEM503
|
3.1
|
60.8
|
1.0
|
CD2
|
B:HIS346
|
3.2
|
51.9
|
1.0
|
CHB
|
B:HEM503
|
3.2
|
57.4
|
1.0
|
CHD
|
B:HEM503
|
3.4
|
53.7
|
1.0
|
CHC
|
B:HEM503
|
3.4
|
48.2
|
1.0
|
CHA
|
B:HEM503
|
3.4
|
60.9
|
1.0
|
CE1
|
B:HIS346
|
3.5
|
55.4
|
1.0
|
C
|
B:ALA264
|
4.0
|
55.1
|
1.0
|
N
|
B:GLY265
|
4.0
|
52.0
|
1.0
|
CA
|
B:ALA264
|
4.1
|
50.6
|
1.0
|
C3A
|
B:HEM503
|
4.1
|
66.0
|
1.0
|
C2B
|
B:HEM503
|
4.1
|
46.3
|
1.0
|
C3B
|
B:HEM503
|
4.2
|
46.0
|
1.0
|
C2A
|
B:HEM503
|
4.2
|
66.7
|
1.0
|
C3C
|
B:HEM503
|
4.2
|
48.8
|
1.0
|
C2C
|
B:HEM503
|
4.2
|
47.0
|
1.0
|
C2D
|
B:HEM503
|
4.3
|
56.0
|
1.0
|
C3D
|
B:HEM503
|
4.3
|
59.5
|
1.0
|
CG
|
B:HIS346
|
4.4
|
52.4
|
1.0
|
O
|
B:ALA264
|
4.5
|
54.7
|
1.0
|
ND1
|
B:HIS346
|
4.5
|
54.4
|
1.0
|
CA
|
B:GLY265
|
4.6
|
56.3
|
1.0
|
N
|
B:ALA264
|
4.8
|
53.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 6tue
Go back to
Iron Binding Sites List in 6tue
Iron binding site 3 out
of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe505
b:64.2
occ:1.00
|
FE
|
C:HEM505
|
0.0
|
64.2
|
1.0
|
NB
|
C:HEM505
|
1.9
|
57.8
|
1.0
|
ND
|
C:HEM505
|
2.0
|
64.3
|
1.0
|
NC
|
C:HEM505
|
2.0
|
54.7
|
1.0
|
NA
|
C:HEM505
|
2.0
|
67.4
|
1.0
|
NE2
|
C:HIS346
|
2.6
|
65.4
|
1.0
|
C1B
|
C:HEM505
|
2.9
|
59.8
|
1.0
|
C4B
|
C:HEM505
|
3.0
|
50.8
|
1.0
|
C1D
|
C:HEM505
|
3.0
|
59.2
|
1.0
|
C4C
|
C:HEM505
|
3.0
|
56.4
|
1.0
|
C4A
|
C:HEM505
|
3.0
|
67.4
|
1.0
|
C1C
|
C:HEM505
|
3.1
|
47.4
|
1.0
|
C4D
|
C:HEM505
|
3.1
|
66.7
|
1.0
|
C1A
|
C:HEM505
|
3.1
|
69.6
|
1.0
|
CD2
|
C:HIS346
|
3.2
|
60.0
|
1.0
|
CHB
|
C:HEM505
|
3.3
|
62.4
|
1.0
|
CHD
|
C:HEM505
|
3.3
|
58.5
|
1.0
|
CHC
|
C:HEM505
|
3.4
|
48.1
|
1.0
|
CHA
|
C:HEM505
|
3.5
|
68.6
|
1.0
|
CB
|
C:ALA264
|
3.8
|
57.5
|
1.0
|
CE1
|
C:HIS346
|
3.8
|
65.1
|
1.0
|
O
|
C:HOH621
|
4.0
|
48.1
|
1.0
|
C2B
|
C:HEM505
|
4.1
|
58.1
|
1.0
|
C3B
|
C:HEM505
|
4.2
|
54.3
|
1.0
|
C2D
|
C:HEM505
|
4.2
|
59.3
|
1.0
|
C3C
|
C:HEM505
|
4.2
|
49.8
|
1.0
|
C3A
|
C:HEM505
|
4.2
|
73.4
|
1.0
|
C3D
|
C:HEM505
|
4.3
|
62.8
|
1.0
|
C2C
|
C:HEM505
|
4.3
|
47.4
|
1.0
|
C2A
|
C:HEM505
|
4.3
|
75.9
|
1.0
|
N
|
C:GLY265
|
4.3
|
57.1
|
1.0
|
C
|
C:ALA264
|
4.3
|
55.4
|
1.0
|
CG
|
C:HIS346
|
4.5
|
61.8
|
1.0
|
CA
|
C:ALA264
|
4.5
|
53.6
|
1.0
|
O
|
C:ALA264
|
4.7
|
54.5
|
1.0
|
ND1
|
C:HIS346
|
4.7
|
68.0
|
1.0
|
CA
|
C:GLY265
|
4.8
|
57.2
|
1.0
|
N
|
C:ALA264
|
4.9
|
52.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 6tue
Go back to
Iron Binding Sites List in 6tue
Iron binding site 4 out
of 4 in the Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe504
b:61.7
occ:1.00
|
FE
|
D:HEM504
|
0.0
|
61.7
|
1.0
|
NB
|
D:HEM504
|
1.9
|
54.3
|
1.0
|
ND
|
D:HEM504
|
2.0
|
64.6
|
1.0
|
NC
|
D:HEM504
|
2.0
|
57.1
|
1.0
|
NA
|
D:HEM504
|
2.1
|
63.5
|
1.0
|
NE2
|
D:HIS346
|
2.5
|
57.5
|
1.0
|
C1B
|
D:HEM504
|
2.9
|
51.0
|
1.0
|
C4A
|
D:HEM504
|
2.9
|
62.1
|
1.0
|
C1D
|
D:HEM504
|
3.0
|
62.1
|
1.0
|
C4B
|
D:HEM504
|
3.0
|
50.9
|
1.0
|
C4C
|
D:HEM504
|
3.0
|
57.1
|
1.0
|
C1C
|
D:HEM504
|
3.1
|
49.8
|
1.0
|
C4D
|
D:HEM504
|
3.1
|
65.2
|
1.0
|
C1A
|
D:HEM504
|
3.1
|
65.6
|
1.0
|
CD2
|
D:HIS346
|
3.1
|
55.5
|
1.0
|
CHB
|
D:HEM504
|
3.3
|
54.9
|
1.0
|
CHD
|
D:HEM504
|
3.4
|
57.0
|
1.0
|
CB
|
D:ALA264
|
3.4
|
56.6
|
1.0
|
CHC
|
D:HEM504
|
3.4
|
46.1
|
1.0
|
CHA
|
D:HEM504
|
3.5
|
65.0
|
1.0
|
CE1
|
D:HIS346
|
3.6
|
64.1
|
1.0
|
C
|
D:ALA264
|
4.1
|
54.2
|
1.0
|
C2B
|
D:HEM504
|
4.1
|
52.0
|
1.0
|
C3A
|
D:HEM504
|
4.1
|
66.6
|
1.0
|
C3B
|
D:HEM504
|
4.2
|
51.6
|
1.0
|
C2D
|
D:HEM504
|
4.2
|
57.3
|
1.0
|
C2A
|
D:HEM504
|
4.2
|
67.3
|
1.0
|
O
|
D:ALA264
|
4.2
|
52.7
|
1.0
|
C3C
|
D:HEM504
|
4.3
|
53.1
|
1.0
|
C3D
|
D:HEM504
|
4.3
|
62.0
|
1.0
|
C2C
|
D:HEM504
|
4.3
|
50.8
|
1.0
|
N
|
D:GLY265
|
4.3
|
53.1
|
1.0
|
CA
|
D:ALA264
|
4.4
|
57.7
|
1.0
|
CG
|
D:HIS346
|
4.4
|
56.5
|
1.0
|
O
|
D:HOH641
|
4.5
|
49.4
|
1.0
|
CG1
|
D:VAL350
|
4.5
|
57.5
|
1.0
|
CA
|
D:GLY265
|
4.6
|
53.1
|
1.0
|
ND1
|
D:HIS346
|
4.6
|
62.8
|
1.0
|
|
Reference:
M.Mirgaux,
J.Wouters.
Structure of Human Indoleamine-2,3-Dioxygenase 1 (Hido) with A Complete Jk Loop To Be Published.
Page generated: Sun Dec 13 17:12:34 2020
|