Iron in PDB 7yxt: Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
Enzymatic activity of Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
All present enzymatic activity of Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment:
1.13.11.52;
Protein crystallography data
The structure of Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment, PDB code: 7yxt
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)
|
49.07 /
2.48
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.04,
117.61,
217.18,
90,
90,
90
|
R / Rfree (%)
|
19.6 /
25.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
(pdb code 7yxt). 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 Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment, PDB code: 7yxt:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7yxt
Go back to
Iron Binding Sites List in 7yxt
Iron binding site 1 out
of 4 in the Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
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 Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:63.2
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
63.2
|
1.0
|
NC
|
A:HEM501
|
2.0
|
60.1
|
1.0
|
ND
|
A:HEM501
|
2.0
|
62.5
|
1.0
|
NA
|
A:HEM501
|
2.1
|
59.7
|
1.0
|
NB
|
A:HEM501
|
2.2
|
57.3
|
1.0
|
NE2
|
A:HIS346
|
2.3
|
58.6
|
1.0
|
C4C
|
A:HEM501
|
2.9
|
60.4
|
1.0
|
C1D
|
A:HEM501
|
2.9
|
62.8
|
1.0
|
C4D
|
A:HEM501
|
3.0
|
65.6
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
51.8
|
1.0
|
C4A
|
A:HEM501
|
3.1
|
58.4
|
1.0
|
C1A
|
A:HEM501
|
3.1
|
62.3
|
1.0
|
CE1
|
A:HIS346
|
3.1
|
57.9
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
55.8
|
1.0
|
C4B
|
A:HEM501
|
3.2
|
49.2
|
1.0
|
CD2
|
A:HIS346
|
3.2
|
61.1
|
1.0
|
CHD
|
A:HEM501
|
3.2
|
58.9
|
1.0
|
CB
|
A:ALA264
|
3.4
|
58.5
|
1.0
|
CHA
|
A:HEM501
|
3.5
|
63.1
|
1.0
|
CHB
|
A:HEM501
|
3.5
|
56.0
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
49.4
|
1.0
|
C
|
A:ALA264
|
3.9
|
65.6
|
1.0
|
N
|
A:GLY265
|
4.1
|
61.8
|
1.0
|
C3C
|
A:HEM501
|
4.1
|
55.2
|
1.0
|
O
|
A:ALA264
|
4.2
|
62.3
|
1.0
|
C2D
|
A:HEM501
|
4.2
|
67.2
|
1.0
|
C2C
|
A:HEM501
|
4.2
|
53.6
|
1.0
|
ND1
|
A:HIS346
|
4.2
|
59.5
|
1.0
|
C3D
|
A:HEM501
|
4.2
|
72.0
|
1.0
|
CA
|
A:ALA264
|
4.2
|
63.5
|
1.0
|
CG
|
A:HIS346
|
4.3
|
56.6
|
1.0
|
C3A
|
A:HEM501
|
4.3
|
61.4
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
60.5
|
1.0
|
C2B
|
A:HEM501
|
4.4
|
54.0
|
1.0
|
C3B
|
A:HEM501
|
4.4
|
51.9
|
1.0
|
CA
|
A:GLY265
|
4.4
|
57.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 7yxt
Go back to
Iron Binding Sites List in 7yxt
Iron binding site 2 out
of 4 in the Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
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 Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:61.0
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
61.0
|
1.0
|
NE2
|
B:HIS346
|
2.0
|
58.8
|
1.0
|
NC
|
B:HEM501
|
2.0
|
62.1
|
1.0
|
ND
|
B:HEM501
|
2.0
|
66.0
|
1.0
|
NA
|
B:HEM501
|
2.1
|
56.3
|
1.0
|
NB
|
B:HEM501
|
2.2
|
59.5
|
1.0
|
O
|
B:ALA264
|
2.3
|
57.6
|
0.8
|
CD2
|
B:HIS346
|
2.9
|
60.2
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
58.5
|
1.0
|
C1C
|
B:HEM501
|
3.0
|
53.5
|
1.0
|
C1D
|
B:HEM501
|
3.1
|
64.3
|
1.0
|
C4D
|
B:HEM501
|
3.1
|
67.4
|
1.0
|
CE1
|
B:HIS346
|
3.1
|
63.9
|
1.0
|
C1A
|
B:HEM501
|
3.1
|
60.6
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
55.0
|
1.0
|
C4A
|
B:HEM501
|
3.2
|
56.7
|
1.0
|
C1B
|
B:HEM501
|
3.2
|
60.2
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
56.3
|
1.0
|
CHA
|
B:HEM501
|
3.4
|
64.5
|
1.0
|
CHC
|
B:HEM501
|
3.4
|
52.1
|
1.0
|
C
|
B:ALA264
|
3.6
|
59.2
|
0.8
|
CHB
|
B:HEM501
|
3.6
|
58.3
|
1.0
|
CB
|
B:ALA264
|
3.6
|
57.2
|
0.2
|
C
|
B:ALA264
|
4.0
|
57.2
|
0.2
|
CG
|
B:HIS346
|
4.1
|
62.0
|
1.0
|
CB
|
B:ALA264
|
4.1
|
55.2
|
0.8
|
O
|
B:ALA264
|
4.1
|
55.2
|
0.2
|
ND1
|
B:HIS346
|
4.1
|
65.5
|
1.0
|
C3C
|
B:HEM501
|
4.2
|
57.5
|
1.0
|
C2C
|
B:HEM501
|
4.2
|
54.9
|
1.0
|
C2D
|
B:HEM501
|
4.3
|
69.0
|
1.0
|
C3D
|
B:HEM501
|
4.3
|
70.5
|
1.0
|
N
|
B:GLY265
|
4.3
|
57.0
|
0.2
|
C2A
|
B:HEM501
|
4.4
|
61.9
|
1.0
|
CA
|
B:ALA264
|
4.4
|
57.0
|
0.2
|
C3B
|
B:HEM501
|
4.4
|
58.1
|
1.0
|
CA
|
B:ALA264
|
4.4
|
57.1
|
0.8
|
C3A
|
B:HEM501
|
4.4
|
58.0
|
1.0
|
C2B
|
B:HEM501
|
4.4
|
58.8
|
1.0
|
CA
|
B:GLY265
|
4.5
|
56.5
|
0.2
|
N
|
B:GLY265
|
4.5
|
57.0
|
0.8
|
CA
|
B:GLY265
|
4.6
|
56.4
|
0.8
|
O
|
B:HOH684
|
4.8
|
52.3
|
1.0
|
CG2
|
B:VAL350
|
5.0
|
58.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 7yxt
Go back to
Iron Binding Sites List in 7yxt
Iron binding site 3 out
of 4 in the Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
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 Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:58.4
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
58.4
|
1.0
|
NC
|
C:HEM501
|
2.0
|
55.8
|
1.0
|
ND
|
C:HEM501
|
2.1
|
60.8
|
1.0
|
NB
|
C:HEM501
|
2.1
|
52.6
|
1.0
|
NA
|
C:HEM501
|
2.1
|
55.0
|
1.0
|
NE2
|
C:HIS346
|
2.3
|
53.2
|
1.0
|
C4C
|
C:HEM501
|
3.0
|
52.5
|
1.0
|
C1D
|
C:HEM501
|
3.0
|
59.1
|
1.0
|
C1C
|
C:HEM501
|
3.0
|
50.6
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
53.5
|
1.0
|
C4D
|
C:HEM501
|
3.1
|
61.6
|
1.0
|
C4A
|
C:HEM501
|
3.1
|
51.5
|
1.0
|
C1B
|
C:HEM501
|
3.2
|
51.6
|
1.0
|
C1A
|
C:HEM501
|
3.2
|
51.3
|
1.0
|
CE1
|
C:HIS346
|
3.2
|
46.2
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
53.9
|
1.0
|
CD2
|
C:HIS346
|
3.4
|
50.8
|
1.0
|
CHC
|
C:HEM501
|
3.4
|
51.6
|
1.0
|
CB
|
C:ALA264
|
3.5
|
62.2
|
1.0
|
CHB
|
C:HEM501
|
3.5
|
52.4
|
1.0
|
CHA
|
C:HEM501
|
3.5
|
54.1
|
1.0
|
C
|
C:ALA264
|
4.1
|
69.2
|
1.0
|
N
|
C:GLY265
|
4.1
|
60.3
|
1.0
|
C3C
|
C:HEM501
|
4.2
|
47.5
|
1.0
|
C2C
|
C:HEM501
|
4.2
|
54.2
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
59.9
|
1.0
|
CA
|
C:ALA264
|
4.3
|
68.6
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
61.9
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
49.0
|
1.0
|
ND1
|
C:HIS346
|
4.4
|
51.6
|
1.0
|
C2B
|
C:HEM501
|
4.4
|
50.8
|
1.0
|
C3A
|
C:HEM501
|
4.4
|
53.9
|
1.0
|
C2A
|
C:HEM501
|
4.4
|
52.1
|
1.0
|
O
|
C:ALA264
|
4.4
|
65.5
|
1.0
|
CG
|
C:HIS346
|
4.5
|
48.0
|
1.0
|
CA
|
C:GLY265
|
4.5
|
51.1
|
1.0
|
N
|
C:ALA264
|
4.8
|
67.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 7yxt
Go back to
Iron Binding Sites List in 7yxt
Iron binding site 4 out
of 4 in the Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment
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 Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:52.9
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
52.9
|
1.0
|
ND
|
D:HEM501
|
2.0
|
52.5
|
1.0
|
NC
|
D:HEM501
|
2.0
|
52.2
|
1.0
|
NE2
|
D:HIS346
|
2.1
|
52.6
|
1.0
|
NB
|
D:HEM501
|
2.1
|
47.0
|
1.0
|
NA
|
D:HEM501
|
2.1
|
49.7
|
1.0
|
O
|
D:ALA264
|
2.3
|
55.4
|
0.5
|
C1D
|
D:HEM501
|
3.0
|
57.0
|
1.0
|
CE1
|
D:HIS346
|
3.0
|
46.1
|
1.0
|
C4C
|
D:HEM501
|
3.0
|
53.6
|
1.0
|
C4D
|
D:HEM501
|
3.0
|
54.8
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
47.1
|
1.0
|
CD2
|
D:HIS346
|
3.1
|
48.1
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
52.0
|
1.0
|
C1B
|
D:HEM501
|
3.1
|
51.5
|
1.0
|
C1A
|
D:HEM501
|
3.1
|
51.7
|
1.0
|
C4A
|
D:HEM501
|
3.2
|
50.0
|
1.0
|
CHD
|
D:HEM501
|
3.3
|
56.4
|
1.0
|
CHC
|
D:HEM501
|
3.4
|
50.2
|
1.0
|
C
|
D:ALA264
|
3.4
|
55.0
|
0.5
|
CHA
|
D:HEM501
|
3.5
|
51.5
|
1.0
|
CHB
|
D:HEM501
|
3.5
|
53.4
|
1.0
|
CB
|
D:ALA264
|
3.6
|
51.4
|
0.5
|
CB
|
D:ALA264
|
4.0
|
54.2
|
0.5
|
ND1
|
D:HIS346
|
4.1
|
45.4
|
1.0
|
N
|
D:GLY265
|
4.2
|
53.7
|
0.5
|
CG
|
D:HIS346
|
4.2
|
46.1
|
1.0
|
C2D
|
D:HEM501
|
4.2
|
59.5
|
1.0
|
C
|
D:ALA264
|
4.2
|
54.5
|
0.5
|
CA
|
D:ALA264
|
4.2
|
54.9
|
0.5
|
C3C
|
D:HEM501
|
4.2
|
50.4
|
1.0
|
C3D
|
D:HEM501
|
4.2
|
59.4
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
50.3
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
51.6
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
53.3
|
1.0
|
C2A
|
D:HEM501
|
4.4
|
52.1
|
1.0
|
C3A
|
D:HEM501
|
4.4
|
52.6
|
1.0
|
N
|
D:GLY265
|
4.4
|
54.5
|
0.5
|
CA
|
D:ALA264
|
4.5
|
53.1
|
0.5
|
CA
|
D:GLY265
|
4.6
|
52.1
|
0.5
|
O
|
D:HOH699
|
4.6
|
59.1
|
0.9
|
O
|
D:ALA264
|
4.6
|
52.0
|
0.5
|
CA
|
D:GLY265
|
4.9
|
52.5
|
0.5
|
|
Reference:
M.Mirgaux,
J.Wouters.
Crystal Structure of Human Indoleamine-2,3-Dioxygenase 1 (HIDO1) with Different Conformations For G261-G265 Fragment To Be Published.
Page generated: Fri Aug 9 12:29:24 2024
|