Iron in PDB 6pyy: Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
Enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
All present enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site:
1.13.11.11;
Protein crystallography data
The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site, PDB code: 6pyy
was solved by
K.N.Pham,
A.Lewis-Ballester,
S.R.Yeh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.90 /
2.40
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
144.188,
154.037,
87.973,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.1 /
23.8
|
Other elements in 6pyy:
The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
(pdb code 6pyy). 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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site, PDB code: 6pyy:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6pyy
Go back to
Iron Binding Sites List in 6pyy
Iron binding site 1 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:47.5
occ:1.00
|
FE
|
A:HEM401
|
0.0
|
47.5
|
1.0
|
ND
|
A:HEM401
|
1.9
|
48.3
|
1.0
|
NA
|
A:HEM401
|
2.0
|
51.7
|
1.0
|
NE2
|
A:HIS328
|
2.0
|
46.2
|
1.0
|
NC
|
A:HEM401
|
2.1
|
45.3
|
1.0
|
NB
|
A:HEM401
|
2.1
|
45.6
|
1.0
|
CE1
|
A:HIS328
|
2.9
|
47.9
|
1.0
|
C1D
|
A:HEM401
|
2.9
|
47.1
|
1.0
|
C4D
|
A:HEM401
|
2.9
|
47.7
|
1.0
|
C1A
|
A:HEM401
|
3.0
|
48.4
|
1.0
|
C4A
|
A:HEM401
|
3.0
|
51.8
|
1.0
|
C4C
|
A:HEM401
|
3.0
|
44.7
|
1.0
|
C1B
|
A:HEM401
|
3.1
|
51.6
|
1.0
|
C4B
|
A:HEM401
|
3.1
|
43.8
|
1.0
|
C1C
|
A:HEM401
|
3.1
|
44.7
|
1.0
|
CD2
|
A:HIS328
|
3.2
|
48.5
|
1.0
|
CHD
|
A:HEM401
|
3.4
|
46.0
|
1.0
|
CHA
|
A:HEM401
|
3.4
|
45.4
|
1.0
|
CHB
|
A:HEM401
|
3.4
|
52.6
|
1.0
|
CHC
|
A:HEM401
|
3.5
|
42.9
|
1.0
|
CD1
|
A:H7S402
|
3.9
|
72.4
|
1.0
|
NE1
|
A:H7S402
|
4.0
|
65.8
|
1.0
|
ND1
|
A:HIS328
|
4.1
|
44.6
|
1.0
|
C2D
|
A:HEM401
|
4.2
|
46.2
|
1.0
|
C3D
|
A:HEM401
|
4.2
|
50.7
|
1.0
|
C3A
|
A:HEM401
|
4.2
|
53.1
|
1.0
|
C2A
|
A:HEM401
|
4.2
|
49.7
|
1.0
|
CG
|
A:HIS328
|
4.2
|
46.1
|
1.0
|
C3C
|
A:HEM401
|
4.2
|
46.2
|
1.0
|
C2C
|
A:HEM401
|
4.3
|
44.8
|
1.0
|
C2B
|
A:HEM401
|
4.3
|
50.3
|
1.0
|
C3B
|
A:HEM401
|
4.4
|
48.8
|
1.0
|
CA
|
A:GLY152
|
4.5
|
68.5
|
1.0
|
O7
|
A:H7S402
|
4.7
|
80.2
|
1.0
|
N
|
A:GLY152
|
4.7
|
64.5
|
1.0
|
CG2
|
A:VAL332
|
4.8
|
53.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 6pyy
Go back to
Iron Binding Sites List in 6pyy
Iron binding site 2 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:44.9
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
44.9
|
1.0
|
ND
|
B:HEM401
|
1.9
|
41.5
|
1.0
|
NA
|
B:HEM401
|
2.0
|
44.2
|
1.0
|
NE2
|
B:HIS328
|
2.1
|
53.0
|
1.0
|
NC
|
B:HEM401
|
2.1
|
41.8
|
1.0
|
NB
|
B:HEM401
|
2.1
|
39.1
|
1.0
|
CE1
|
B:HIS328
|
2.9
|
50.3
|
1.0
|
C1D
|
B:HEM401
|
2.9
|
38.8
|
1.0
|
C4D
|
B:HEM401
|
2.9
|
38.5
|
1.0
|
C1A
|
B:HEM401
|
3.0
|
44.8
|
1.0
|
C4C
|
B:HEM401
|
3.0
|
43.8
|
1.0
|
C1B
|
B:HEM401
|
3.0
|
43.4
|
1.0
|
C4A
|
B:HEM401
|
3.1
|
43.7
|
1.0
|
C4B
|
B:HEM401
|
3.1
|
39.9
|
1.0
|
C1C
|
B:HEM401
|
3.1
|
39.5
|
1.0
|
CD2
|
B:HIS328
|
3.2
|
51.9
|
1.0
|
CHD
|
B:HEM401
|
3.4
|
41.5
|
1.0
|
CHA
|
B:HEM401
|
3.4
|
40.2
|
1.0
|
CHB
|
B:HEM401
|
3.5
|
42.5
|
1.0
|
CHC
|
B:HEM401
|
3.5
|
39.1
|
1.0
|
CD1
|
B:H7S402
|
3.9
|
59.9
|
1.0
|
ND1
|
B:HIS328
|
4.1
|
47.5
|
1.0
|
NE1
|
B:H7S402
|
4.1
|
57.9
|
1.0
|
C3D
|
B:HEM401
|
4.2
|
40.1
|
1.0
|
C2D
|
B:HEM401
|
4.2
|
37.8
|
1.0
|
C2A
|
B:HEM401
|
4.2
|
45.9
|
1.0
|
C3A
|
B:HEM401
|
4.2
|
45.3
|
1.0
|
C3C
|
B:HEM401
|
4.3
|
42.7
|
1.0
|
C2C
|
B:HEM401
|
4.3
|
41.5
|
1.0
|
C2B
|
B:HEM401
|
4.3
|
42.2
|
1.0
|
CG
|
B:HIS328
|
4.3
|
48.1
|
1.0
|
C3B
|
B:HEM401
|
4.3
|
41.1
|
1.0
|
CG2
|
B:VAL332
|
4.7
|
50.2
|
1.0
|
O7
|
B:H7S402
|
4.7
|
71.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 6pyy
Go back to
Iron Binding Sites List in 6pyy
Iron binding site 3 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:53.1
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
53.1
|
1.0
|
ND
|
C:HEM401
|
1.9
|
53.6
|
1.0
|
NA
|
C:HEM401
|
2.0
|
61.5
|
1.0
|
NE2
|
C:HIS328
|
2.1
|
46.9
|
1.0
|
NC
|
C:HEM401
|
2.1
|
53.9
|
1.0
|
NB
|
C:HEM401
|
2.1
|
52.4
|
1.0
|
C1D
|
C:HEM401
|
2.9
|
57.1
|
1.0
|
CE1
|
C:HIS328
|
2.9
|
50.2
|
1.0
|
C4D
|
C:HEM401
|
2.9
|
53.2
|
1.0
|
C4C
|
C:HEM401
|
3.0
|
53.4
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
53.9
|
1.0
|
C4B
|
C:HEM401
|
3.1
|
52.6
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
49.6
|
1.0
|
C4A
|
C:HEM401
|
3.1
|
54.1
|
1.0
|
C1B
|
C:HEM401
|
3.1
|
52.2
|
1.0
|
CD2
|
C:HIS328
|
3.2
|
41.6
|
1.0
|
CHD
|
C:HEM401
|
3.3
|
52.7
|
1.0
|
CHA
|
C:HEM401
|
3.4
|
50.1
|
1.0
|
CHC
|
C:HEM401
|
3.5
|
54.8
|
1.0
|
CHB
|
C:HEM401
|
3.5
|
50.1
|
1.0
|
CD1
|
C:H7S402
|
3.7
|
77.5
|
1.0
|
NE1
|
C:H7S402
|
3.9
|
74.9
|
1.0
|
ND1
|
C:HIS328
|
4.1
|
47.1
|
1.0
|
C2D
|
C:HEM401
|
4.1
|
52.3
|
1.0
|
C3D
|
C:HEM401
|
4.2
|
53.7
|
1.0
|
C2A
|
C:HEM401
|
4.2
|
54.1
|
1.0
|
C3C
|
C:HEM401
|
4.3
|
50.9
|
1.0
|
CG
|
C:HIS328
|
4.3
|
43.4
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
46.7
|
1.0
|
C3A
|
C:HEM401
|
4.3
|
55.9
|
1.0
|
C2B
|
C:HEM401
|
4.4
|
52.4
|
1.0
|
C3B
|
C:HEM401
|
4.4
|
49.9
|
1.0
|
O7
|
C:H7S402
|
4.6
|
86.7
|
1.0
|
CG2
|
C:VAL332
|
4.7
|
53.3
|
1.0
|
CA
|
C:GLY152
|
4.8
|
61.6
|
1.0
|
N
|
C:GLY152
|
4.9
|
56.3
|
1.0
|
CG
|
C:H7S402
|
5.0
|
79.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 6pyy
Go back to
Iron Binding Sites List in 6pyy
Iron binding site 4 out
of 4 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site
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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:40.2
occ:1.00
|
FE
|
D:HEM401
|
0.0
|
40.2
|
1.0
|
ND
|
D:HEM401
|
1.9
|
43.5
|
1.0
|
NA
|
D:HEM401
|
2.0
|
42.0
|
1.0
|
NE2
|
D:HIS328
|
2.1
|
48.2
|
1.0
|
NC
|
D:HEM401
|
2.1
|
43.5
|
1.0
|
NB
|
D:HEM401
|
2.1
|
40.2
|
1.0
|
C1D
|
D:HEM401
|
2.9
|
42.1
|
1.0
|
C4D
|
D:HEM401
|
2.9
|
41.4
|
1.0
|
CE1
|
D:HIS328
|
3.0
|
45.5
|
1.0
|
C1A
|
D:HEM401
|
3.0
|
41.9
|
1.0
|
C4A
|
D:HEM401
|
3.1
|
41.2
|
1.0
|
C4C
|
D:HEM401
|
3.1
|
38.1
|
1.0
|
C1B
|
D:HEM401
|
3.1
|
43.7
|
1.0
|
C4B
|
D:HEM401
|
3.1
|
44.5
|
1.0
|
C1C
|
D:HEM401
|
3.1
|
41.4
|
1.0
|
CD2
|
D:HIS328
|
3.2
|
46.0
|
1.0
|
CHA
|
D:HEM401
|
3.3
|
43.5
|
1.0
|
CHD
|
D:HEM401
|
3.4
|
37.9
|
1.0
|
CHB
|
D:HEM401
|
3.5
|
40.8
|
1.0
|
CHC
|
D:HEM401
|
3.5
|
42.1
|
1.0
|
CD1
|
D:H7S402
|
3.7
|
71.2
|
1.0
|
NE1
|
D:H7S402
|
3.9
|
66.3
|
1.0
|
ND1
|
D:HIS328
|
4.1
|
41.6
|
1.0
|
C2D
|
D:HEM401
|
4.1
|
43.2
|
1.0
|
C3D
|
D:HEM401
|
4.1
|
42.8
|
1.0
|
C2A
|
D:HEM401
|
4.2
|
44.2
|
1.0
|
C3A
|
D:HEM401
|
4.2
|
47.7
|
1.0
|
CG
|
D:HIS328
|
4.3
|
44.5
|
1.0
|
C3C
|
D:HEM401
|
4.3
|
37.7
|
1.0
|
C2C
|
D:HEM401
|
4.3
|
40.1
|
1.0
|
C2B
|
D:HEM401
|
4.3
|
46.8
|
1.0
|
C3B
|
D:HEM401
|
4.3
|
41.5
|
1.0
|
CA
|
D:GLY152
|
4.6
|
56.3
|
1.0
|
N
|
D:GLY152
|
4.8
|
58.5
|
1.0
|
CG2
|
D:VAL332
|
4.8
|
43.5
|
1.0
|
O7
|
D:H7S402
|
5.0
|
64.2
|
1.0
|
CG
|
D:H7S402
|
5.0
|
69.4
|
1.0
|
|
Reference:
K.N.Pham,
A.Lewis-Ballester,
S.R.Yeh.
Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J.Am.Chem.Soc. V. 141 18771 2019.
ISSN: ESSN 1520-5126
PubMed: 31682426
DOI: 10.1021/JACS.9B08871
Page generated: Wed Aug 7 06:44:54 2024
|