Iron in PDB 6e45: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State:
1.13.11.52;
Protein crystallography data
The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State, PDB code: 6e45
was solved by
S.Luo,
L.Tong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.88 /
2.00
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.969,
196.538,
116.207,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
22.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
(pdb code 6e45). 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 (IDO1) Free Enzyme in the Ferrous State, PDB code: 6e45:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6e45
Go back to
Iron Binding Sites List in 6e45
Iron binding site 1 out
of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
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 (IDO1) Free Enzyme in the Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:33.1
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
33.1
|
1.0
|
NA
|
A:HEM501
|
2.0
|
30.7
|
1.0
|
NC
|
A:HEM501
|
2.0
|
29.9
|
1.0
|
NB
|
A:HEM501
|
2.1
|
28.6
|
1.0
|
ND
|
A:HEM501
|
2.1
|
30.3
|
1.0
|
NE2
|
A:HIS346
|
2.2
|
35.0
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
32.3
|
1.0
|
C1B
|
A:HEM501
|
3.0
|
29.3
|
1.0
|
C4C
|
A:HEM501
|
3.0
|
31.1
|
1.0
|
C1A
|
A:HEM501
|
3.1
|
34.1
|
1.0
|
C1D
|
A:HEM501
|
3.1
|
29.6
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
29.8
|
1.0
|
C4B
|
A:HEM501
|
3.1
|
28.3
|
1.0
|
CD2
|
A:HIS346
|
3.1
|
34.5
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
30.8
|
1.0
|
CE1
|
A:HIS346
|
3.2
|
37.7
|
1.0
|
CHB
|
A:HEM501
|
3.4
|
29.4
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
31.1
|
1.0
|
CHA
|
A:HEM501
|
3.5
|
31.9
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
29.4
|
1.0
|
CB
|
A:ALA264
|
4.0
|
31.6
|
1.0
|
C3A
|
A:HEM501
|
4.2
|
35.7
|
1.0
|
C2B
|
A:HEM501
|
4.2
|
30.5
|
1.0
|
ND1
|
A:HIS346
|
4.3
|
33.4
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
29.1
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
33.4
|
1.0
|
O
|
A:HOH756
|
4.3
|
36.5
|
1.0
|
CG
|
A:HIS346
|
4.3
|
35.0
|
1.0
|
C3B
|
A:HEM501
|
4.3
|
28.8
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
31.7
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
36.2
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
32.1
|
1.0
|
N
|
A:GLY265
|
4.5
|
29.8
|
1.0
|
C
|
A:ALA264
|
4.6
|
30.5
|
1.0
|
CA
|
A:ALA264
|
4.8
|
32.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 6e45
Go back to
Iron Binding Sites List in 6e45
Iron binding site 2 out
of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
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 (IDO1) Free Enzyme in the Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:30.7
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
30.7
|
1.0
|
NA
|
B:HEM501
|
2.0
|
32.2
|
1.0
|
NB
|
B:HEM501
|
2.0
|
28.3
|
1.0
|
NC
|
B:HEM501
|
2.0
|
32.4
|
1.0
|
ND
|
B:HEM501
|
2.1
|
31.0
|
1.0
|
NE2
|
B:HIS346
|
2.2
|
30.8
|
1.0
|
C1B
|
B:HEM501
|
3.0
|
29.4
|
1.0
|
C4A
|
B:HEM501
|
3.0
|
34.4
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
33.4
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
31.1
|
1.0
|
C1A
|
B:HEM501
|
3.1
|
33.7
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
27.9
|
1.0
|
C1D
|
B:HEM501
|
3.1
|
32.6
|
1.0
|
C4D
|
B:HEM501
|
3.1
|
30.5
|
1.0
|
CD2
|
B:HIS346
|
3.1
|
30.8
|
1.0
|
CE1
|
B:HIS346
|
3.2
|
31.1
|
1.0
|
CHB
|
B:HEM501
|
3.3
|
28.7
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
32.1
|
1.0
|
CHC
|
B:HEM501
|
3.5
|
29.9
|
1.0
|
CHA
|
B:HEM501
|
3.5
|
31.6
|
1.0
|
CB
|
B:ALA264
|
3.9
|
29.9
|
1.0
|
C2B
|
B:HEM501
|
4.2
|
29.5
|
1.0
|
C3A
|
B:HEM501
|
4.2
|
34.8
|
1.0
|
C3B
|
B:HEM501
|
4.2
|
29.4
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
29.3
|
1.0
|
ND1
|
B:HIS346
|
4.3
|
30.1
|
1.0
|
C2A
|
B:HEM501
|
4.3
|
36.2
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
32.8
|
1.0
|
CG
|
B:HIS346
|
4.3
|
29.2
|
1.0
|
C2D
|
B:HEM501
|
4.3
|
34.2
|
1.0
|
O
|
B:HOH800
|
4.3
|
35.1
|
1.0
|
C3D
|
B:HEM501
|
4.3
|
30.2
|
1.0
|
N
|
B:GLY265
|
4.6
|
28.4
|
1.0
|
C
|
B:ALA264
|
4.6
|
29.4
|
1.0
|
CA
|
B:ALA264
|
4.8
|
28.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 6e45
Go back to
Iron Binding Sites List in 6e45
Iron binding site 3 out
of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
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 (IDO1) Free Enzyme in the Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:28.9
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
28.9
|
1.0
|
NC
|
C:HEM501
|
2.0
|
25.5
|
1.0
|
NB
|
C:HEM501
|
2.0
|
28.7
|
1.0
|
NA
|
C:HEM501
|
2.1
|
29.6
|
1.0
|
NE2
|
C:HIS346
|
2.1
|
29.7
|
1.0
|
ND
|
C:HEM501
|
2.1
|
29.2
|
1.0
|
C1B
|
C:HEM501
|
3.0
|
28.0
|
1.0
|
CE1
|
C:HIS346
|
3.0
|
29.8
|
1.0
|
C4C
|
C:HEM501
|
3.0
|
26.2
|
1.0
|
C4A
|
C:HEM501
|
3.0
|
30.9
|
1.0
|
CD2
|
C:HIS346
|
3.1
|
26.5
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
26.2
|
1.0
|
C4B
|
C:HEM501
|
3.1
|
27.1
|
1.0
|
C1D
|
C:HEM501
|
3.1
|
28.8
|
1.0
|
C1A
|
C:HEM501
|
3.1
|
33.1
|
1.0
|
C4D
|
C:HEM501
|
3.1
|
29.1
|
1.0
|
CHB
|
C:HEM501
|
3.4
|
30.7
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
28.3
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
25.1
|
1.0
|
CHA
|
C:HEM501
|
3.5
|
31.0
|
1.0
|
CB
|
C:ALA264
|
4.0
|
28.0
|
1.0
|
ND1
|
C:HIS346
|
4.1
|
28.3
|
1.0
|
CG
|
C:HIS346
|
4.2
|
29.9
|
1.0
|
O
|
C:HOH787
|
4.2
|
31.3
|
1.0
|
C2B
|
C:HEM501
|
4.2
|
29.8
|
1.0
|
C3C
|
C:HEM501
|
4.2
|
27.2
|
1.0
|
C3B
|
C:HEM501
|
4.3
|
28.1
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
25.2
|
1.0
|
C3A
|
C:HEM501
|
4.3
|
36.2
|
1.0
|
C2A
|
C:HEM501
|
4.3
|
34.2
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
31.8
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
29.5
|
1.0
|
N
|
C:GLY265
|
4.5
|
27.5
|
1.0
|
C
|
C:ALA264
|
4.6
|
28.2
|
1.0
|
CA
|
C:ALA264
|
4.8
|
29.4
|
1.0
|
CG2
|
C:VAL350
|
4.9
|
28.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 6e45
Go back to
Iron Binding Sites List in 6e45
Iron binding site 4 out
of 4 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 (IDO1) Free Enzyme in the Ferrous State
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 (IDO1) Free Enzyme in the Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:27.4
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
27.4
|
1.0
|
NB
|
D:HEM501
|
2.0
|
26.5
|
1.0
|
NA
|
D:HEM501
|
2.0
|
29.4
|
1.0
|
ND
|
D:HEM501
|
2.0
|
29.6
|
1.0
|
NC
|
D:HEM501
|
2.1
|
27.6
|
1.0
|
NE2
|
D:HIS346
|
2.2
|
25.6
|
1.0
|
C1B
|
D:HEM501
|
3.0
|
25.7
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
30.7
|
1.0
|
C1D
|
D:HEM501
|
3.1
|
27.0
|
1.0
|
CE1
|
D:HIS346
|
3.1
|
28.0
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
27.6
|
1.0
|
C4D
|
D:HEM501
|
3.1
|
29.2
|
1.0
|
C4C
|
D:HEM501
|
3.1
|
28.8
|
1.0
|
C1A
|
D:HEM501
|
3.1
|
30.1
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
25.0
|
1.0
|
CD2
|
D:HIS346
|
3.2
|
28.9
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
26.8
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
28.6
|
1.0
|
CHA
|
D:HEM501
|
3.4
|
30.8
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
25.5
|
1.0
|
O
|
D:HOH765
|
4.0
|
33.0
|
1.0
|
CB
|
D:ALA264
|
4.0
|
28.4
|
1.0
|
ND1
|
D:HIS346
|
4.2
|
25.4
|
1.0
|
C2B
|
D:HEM501
|
4.2
|
26.9
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
26.0
|
1.0
|
CG
|
D:HIS346
|
4.3
|
28.0
|
1.0
|
C3A
|
D:HEM501
|
4.3
|
32.4
|
1.0
|
C2D
|
D:HEM501
|
4.3
|
27.9
|
1.0
|
C3D
|
D:HEM501
|
4.3
|
28.1
|
1.0
|
C2A
|
D:HEM501
|
4.3
|
32.6
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
27.8
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
28.9
|
1.0
|
N
|
D:GLY265
|
4.7
|
26.1
|
1.0
|
C
|
D:ALA264
|
4.7
|
26.2
|
1.0
|
CA
|
D:ALA264
|
4.8
|
26.9
|
1.0
|
|
Reference:
S.Luo,
K.Xu,
S.Xiang,
J.Chen,
C.Chen,
C.Guo,
Y.Tong,
L.Tong.
High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Tue Aug 6 17:18:15 2024
|