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Iron in PDB 6pyz: Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site

Enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site

All present enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active 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, PDB code: 6pyz 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) 29.86 / 2.02
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.648, 154.158, 87.951, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.3

Other elements in 6pyz:

The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site also contains other interesting chemical elements:

Fluorine (F) 4 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 (pdb code 6pyz). 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, PDB code: 6pyz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6pyz

Go back to Iron Binding Sites List in 6pyz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:42.2
occ:1.00
 FE A:HEM401 0.0 42.2 1.0
ND A:HEM401 1.9 41.3 1.0
NA A:HEM401 2.0 46.6 1.0
NC A:HEM401 2.1 39.5 1.0
NB A:HEM401 2.1 42.5 1.0
NE2 A:HIS328 2.2 42.5 1.0
O A:HOH547 2.5 74.1 1.0
C4D A:HEM401 2.9 44.5 1.0
C1D A:HEM401 2.9 41.9 1.0
C1A A:HEM401 3.0 46.6 1.0
C4C A:HEM401 3.0 39.7 1.0
C4A A:HEM401 3.1 46.5 1.0
C4B A:HEM401 3.1 41.8 1.0
C1B A:HEM401 3.1 46.6 1.0
C1C A:HEM401 3.1 41.0 1.0
CE1 A:HIS328 3.1 45.6 1.0
CD2 A:HIS328 3.3 46.5 1.0
CHA A:HEM401 3.4 44.6 1.0
CHD A:HEM401 3.4 40.5 1.0
CHB A:HEM401 3.5 46.5 1.0
CHC A:HEM401 3.5 41.1 1.0
CD1 A:H7S402 3.9 82.1 1.0
NE1 A:H7S402 4.1 76.5 1.0
C3D A:HEM401 4.2 42.0 1.0
C2D A:HEM401 4.2 38.9 1.0
C2A A:HEM401 4.2 49.5 1.0
C3A A:HEM401 4.2 49.4 1.0
ND1 A:HIS328 4.3 40.8 1.0
C3C A:HEM401 4.3 35.6 1.0
C2C A:HEM401 4.3 38.1 1.0
C2B A:HEM401 4.3 47.3 1.0
C3B A:HEM401 4.3 45.6 1.0
CG A:HIS328 4.4 41.8 1.0
CA A:GLY152 4.7 55.7 1.0
CG2 A:VAL332 4.7 52.1 1.0
N A:GLY152 4.8 53.1 1.0
O7 A:H7S402 4.9 85.3 1.0

Iron binding site 2 out of 4 in 6pyz

Go back to Iron Binding Sites List in 6pyz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:43.2
occ:1.00
 FE B:HEM401 0.0 43.2 1.0
ND B:HEM401 1.9 41.2 1.0
NA B:HEM401 2.0 40.8 1.0
NC B:HEM401 2.1 40.7 1.0
NB B:HEM401 2.1 40.5 1.0
NE2 B:HIS328 2.3 44.0 1.0
O B:HOH526 2.5 70.3 1.0
C4D B:HEM401 2.9 37.7 1.0
C1D B:HEM401 2.9 40.6 1.0
C1A B:HEM401 3.0 42.5 1.0
C4B B:HEM401 3.0 40.2 1.0
C4C B:HEM401 3.0 41.4 1.0
C1B B:HEM401 3.1 44.1 1.0
C4A B:HEM401 3.1 43.1 1.0
C1C B:HEM401 3.1 38.9 1.0
CE1 B:HIS328 3.2 42.6 1.0
CD2 B:HIS328 3.3 44.4 1.0
CHA B:HEM401 3.3 39.8 1.0
CHD B:HEM401 3.4 42.2 1.0
CHC B:HEM401 3.5 38.8 1.0
CHB B:HEM401 3.5 44.8 1.0
CD1 B:H7S402 3.8 68.4 1.0
NE1 B:H7S402 4.0 72.1 1.0
C3D B:HEM401 4.2 41.5 1.0
C2D B:HEM401 4.2 38.2 1.0
C2A B:HEM401 4.2 44.1 1.0
C3A B:HEM401 4.3 43.9 1.0
C3C B:HEM401 4.3 40.0 1.0
C2C B:HEM401 4.3 40.8 1.0
C2B B:HEM401 4.3 39.8 1.0
C3B B:HEM401 4.3 38.6 1.0
ND1 B:HIS328 4.3 43.2 1.0
CG B:HIS328 4.4 42.4 1.0
O7 B:H7S402 4.5 77.1 1.0
CG2 B:VAL332 4.7 45.4 1.0
CA B:GLY152 4.9 52.2 1.0
N B:GLY152 5.0 52.2 1.0

Iron binding site 3 out of 4 in 6pyz

Go back to Iron Binding Sites List in 6pyz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:47.7
occ:1.00
 FE C:HEM401 0.0 47.7 1.0
ND C:HEM401 1.9 48.1 1.0
NA C:HEM401 2.0 55.9 1.0
NC C:HEM401 2.1 45.2 1.0
NB C:HEM401 2.1 48.7 1.0
NE2 C:HIS328 2.2 40.1 1.0
C1D C:HEM401 2.9 48.7 1.0
C4D C:HEM401 2.9 48.5 1.0
C1A C:HEM401 3.0 51.7 1.0
C4C C:HEM401 3.1 44.9 1.0
C4A C:HEM401 3.1 53.1 1.0
C1B C:HEM401 3.1 51.2 1.0
C4B C:HEM401 3.1 47.5 1.0
CE1 C:HIS328 3.1 43.3 1.0
C1C C:HEM401 3.1 47.9 1.0
CD2 C:HIS328 3.3 42.3 1.0
CHA C:HEM401 3.4 49.1 1.0
CHD C:HEM401 3.4 44.8 1.0
CHB C:HEM401 3.5 51.8 1.0
CHC C:HEM401 3.5 46.5 1.0
CD1 C:H7S402 3.8 81.5 1.0
NE1 C:H7S402 4.1 80.2 1.0
C2D C:HEM401 4.2 50.2 1.0
C3D C:HEM401 4.2 47.4 1.0
C2A C:HEM401 4.2 54.6 1.0
C3A C:HEM401 4.3 55.0 1.0
ND1 C:HIS328 4.3 41.2 1.0
C3C C:HEM401 4.3 43.9 1.0
C2C C:HEM401 4.3 44.9 1.0
C2B C:HEM401 4.3 50.8 1.0
O7 C:H7S402 4.3 97.3 1.0
C3B C:HEM401 4.4 47.2 1.0
CG C:HIS328 4.4 41.5 1.0
CA C:GLY152 4.8 60.7 1.0
CG2 C:VAL332 4.9 52.6 1.0
N C:GLY152 4.9 56.3 1.0

Iron binding site 4 out of 4 in 6pyz

Go back to Iron Binding Sites List in 6pyz
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:42.3
occ:1.00
 FE D:HEM401 0.0 42.3 1.0
ND D:HEM401 1.9 40.1 1.0
NA D:HEM401 2.0 43.7 1.0
NB D:HEM401 2.1 42.9 1.0
NC D:HEM401 2.1 41.3 1.0
NE2 D:HIS328 2.3 45.8 1.0
C1D D:HEM401 2.9 43.8 1.0
C4D D:HEM401 2.9 43.5 1.0
C1A D:HEM401 3.0 40.2 1.0
C4B D:HEM401 3.0 44.1 1.0
C1B D:HEM401 3.1 44.7 1.0
C4A D:HEM401 3.1 43.1 1.0
C4C D:HEM401 3.1 39.5 1.0
C1C D:HEM401 3.1 41.2 1.0
CE1 D:HIS328 3.2 44.9 1.0
CD2 D:HIS328 3.3 46.8 1.0
CHD D:HEM401 3.4 38.6 1.0
CHA D:HEM401 3.4 41.8 1.0
CHC D:HEM401 3.5 42.9 1.0
CHB D:HEM401 3.5 43.6 1.0
CD1 D:H7S402 3.7 64.2 1.0
NE1 D:H7S402 4.0 62.2 1.0
C2D D:HEM401 4.2 41.3 1.0
C3D D:HEM401 4.2 38.9 1.0
C2A D:HEM401 4.2 46.8 1.0
C3A D:HEM401 4.3 44.8 1.0
C2B D:HEM401 4.3 45.5 1.0
C3B D:HEM401 4.3 40.4 1.0
C2C D:HEM401 4.3 39.3 1.0
C3C D:HEM401 4.3 36.3 1.0
ND1 D:HIS328 4.3 44.9 1.0
CG D:HIS328 4.4 46.0 1.0
CA D:GLY152 4.7 50.7 1.0
O7 D:H7S402 4.7 72.5 1.0
N D:GLY152 4.8 49.1 1.0
CG2 D:VAL332 4.8 44.2 1.0
CG D:H7S402 5.0 68.5 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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