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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:

Fluorine (F) 8 atoms

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

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