Atomistry » Iron » PDB 6ppu-6q9k » 6pyy
Atomistry »
  Iron »
    PDB 6ppu-6q9k »
      6pyy »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy