Atomistry » Fluorine » PDB 6pf9-6q0j » 6pyz
Atomistry »
  Fluorine »
    PDB 6pf9-6q0j »
      6pyz »

Fluorine 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:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6pyz

Go back to Fluorine Binding Sites List in 6pyz
Fluorine 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 Fluorine with other atoms in the F 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:F402

b:79.6
occ:1.00
F8 A:H7S402 0.0 79.6 1.0
CZ3 A:H7S402 1.4 76.7 1.0
CE3 A:H7S402 2.3 77.2 1.0
CH2 A:H7S402 2.4 78.2 1.0
CB A:ALA150 2.9 55.2 1.0
CD2 B:TYR45 3.2 43.6 1.0
CD2 A:H7S402 3.6 82.3 1.0
CZ2 A:H7S402 3.6 80.0 1.0
CE2 B:TYR45 3.7 46.0 1.0
CG B:TYR45 3.8 45.4 1.0
C A:ALA150 3.9 58.6 1.0
CD2 A:LEU147 3.9 62.5 1.0
O A:ALA150 4.0 56.5 1.0
CA A:ALA150 4.0 56.3 1.0
CE2 A:H7S402 4.1 80.0 1.0
CB B:TYR45 4.1 41.2 1.0
O A:LEU147 4.2 51.1 1.0
CB A:LEU147 4.3 62.5 1.0
N A:SER151 4.3 57.7 1.0
CA B:TYR42 4.4 41.9 1.0
CD2 B:LEU40 4.6 65.8 1.0
CG A:LEU147 4.6 62.9 1.0
CZ B:TYR45 4.6 46.9 1.0
CA A:LEU147 4.7 59.9 1.0
CD1 B:TYR45 4.7 47.3 1.0
C A:LEU147 4.8 57.2 1.0
CD2 B:TYR42 4.9 39.1 1.0
CE2 A:PHE72 4.9 37.0 1.0
CG A:H7S402 4.9 83.2 1.0
N B:TYR42 4.9 46.2 1.0
N A:ALA150 5.0 64.3 1.0

Fluorine binding site 2 out of 4 in 6pyz

Go back to Fluorine Binding Sites List in 6pyz
Fluorine 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 Fluorine with other atoms in the F 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:F402

b:74.4
occ:1.00
F8 B:H7S402 0.0 74.4 1.0
CZ3 B:H7S402 1.4 68.8 1.0
CE3 B:H7S402 2.3 68.2 1.0
CH2 B:H7S402 2.4 66.6 1.0
CB B:ALA150 3.1 53.9 1.0
CD2 A:TYR45 3.2 38.5 1.0
CG A:TYR45 3.5 40.0 1.0
CD2 B:H7S402 3.6 69.7 1.0
CZ2 B:H7S402 3.6 68.0 1.0
CB A:TYR45 3.7 40.5 1.0
CE2 A:TYR45 3.8 41.8 1.0
CD2 B:LEU147 4.1 59.6 1.0
CE2 B:H7S402 4.1 70.5 1.0
CA B:ALA150 4.2 56.4 1.0
C B:ALA150 4.2 57.0 1.0
CA A:TYR42 4.3 41.7 1.0
O B:LEU147 4.4 54.9 1.0
CD1 A:TYR45 4.4 41.6 1.0
N B:SER151 4.5 57.4 1.0
O B:ALA150 4.6 58.3 1.0
CB B:LEU147 4.6 58.2 1.0
CD2 A:LEU40 4.7 65.5 1.0
CZ A:TYR45 4.7 41.0 1.0
CD1 A:TYR42 4.7 37.7 1.0
N A:TYR42 4.8 44.0 1.0
CG B:LEU147 4.9 58.0 1.0
CA B:LEU147 4.9 56.5 1.0
O A:TYR42 4.9 36.8 1.0
CG B:H7S402 5.0 67.3 1.0
CE2 B:PHE72 5.0 37.5 1.0
CE1 A:TYR45 5.0 42.9 1.0
CB A:TYR42 5.0 41.7 1.0

Fluorine binding site 3 out of 4 in 6pyz

Go back to Fluorine Binding Sites List in 6pyz
Fluorine 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 Fluorine with other atoms in the F 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:F402

b:78.1
occ:1.00
F8 C:H7S402 0.0 78.1 1.0
CZ3 C:H7S402 1.4 75.0 1.0
CH2 C:H7S402 2.3 71.8 1.0
CE3 C:H7S402 2.3 77.0 1.0
CB C:ALA150 3.0 62.2 1.0
CD2 D:TYR45 3.3 45.8 1.0
CZ2 C:H7S402 3.6 73.8 1.0
CD2 C:H7S402 3.6 78.7 1.0
CG D:TYR45 3.7 46.8 1.0
CE2 D:TYR45 3.8 49.3 1.0
CB D:TYR45 4.0 43.4 1.0
CE2 C:H7S402 4.1 79.7 1.0
C C:ALA150 4.1 67.6 1.0
CA C:ALA150 4.2 62.2 1.0
CD2 C:LEU147 4.2 59.9 1.0
O C:ALA150 4.3 68.8 1.0
CA D:TYR42 4.3 48.6 1.0
O C:LEU147 4.3 56.0 1.0
CB C:LEU147 4.4 60.6 1.0
N C:SER151 4.5 68.2 1.0
CD1 D:TYR45 4.6 47.2 1.0
N D:TYR42 4.7 48.3 1.0
CZ D:TYR45 4.7 48.7 1.0
CG C:LEU147 4.7 59.2 1.0
CD1 D:TYR42 4.8 50.3 1.0
CA C:LEU147 4.8 58.4 1.0
CE2 C:PHE72 4.9 41.0 1.0
CG C:H7S402 5.0 82.8 1.0
CD2 D:LEU40 5.0 68.2 1.0
CD1 C:LEU147 5.0 59.0 1.0
O D:TYR42 5.0 42.8 1.0
CB D:TYR42 5.0 50.2 1.0

Fluorine binding site 4 out of 4 in 6pyz

Go back to Fluorine Binding Sites List in 6pyz
Fluorine 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 Fluorine with other atoms in the F 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:F402

b:70.0
occ:1.00
F8 D:H7S402 0.0 70.0 1.0
CZ3 D:H7S402 1.4 66.7 1.0
CE3 D:H7S402 2.3 62.6 1.0
CH2 D:H7S402 2.4 61.1 1.0
CB D:ALA150 3.1 50.5 1.0
CD2 C:TYR45 3.2 35.8 1.0
CG C:TYR45 3.5 40.4 1.0
CD2 D:H7S402 3.6 66.1 1.0
CZ2 D:H7S402 3.6 61.1 1.0
CE2 C:TYR45 3.7 38.8 1.0
CB C:TYR45 3.9 40.9 1.0
CE2 D:H7S402 4.1 66.3 1.0
CD2 D:LEU147 4.1 51.5 1.0
CB D:LEU147 4.2 50.8 1.0
O D:LEU147 4.3 51.4 1.0
CD1 C:TYR45 4.3 42.0 1.0
CA D:ALA150 4.3 52.4 1.0
C D:ALA150 4.3 53.3 1.0
CA C:TYR42 4.4 43.7 1.0
CZ C:TYR45 4.5 38.0 1.0
O D:ALA150 4.5 51.3 1.0
CD2 C:LEU40 4.5 65.7 1.0
CG D:LEU147 4.6 50.0 1.0
CA D:LEU147 4.6 51.2 1.0
CE1 C:TYR45 4.7 37.5 1.0
N D:SER151 4.8 51.7 1.0
N C:TYR42 4.8 45.7 1.0
CE2 D:PHE72 4.8 40.9 1.0
CD1 D:LEU147 4.9 52.3 1.0
C D:LEU147 4.9 50.9 1.0
CG D:H7S402 4.9 68.5 1.0
CD1 C:TYR42 5.0 43.5 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: Fri Aug 2 00:32:29 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy