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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

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