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Fluorine in PDB 6pz1: Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site

Enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site

All present enzymatic activity of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site:
1.13.11.52;

Protein crystallography data

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site, PDB code: 6pz1 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) 40.00 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.479, 97.858, 131.966, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27

Other elements in 6pz1:

The structure of Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site (pdb code 6pz1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site, PDB code: 6pz1:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6pz1

Go back to Fluorine Binding Sites List in 6pz1
Fluorine binding site 1 out of 3 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si 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 Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:0.8
occ:1.00
 F1 A:AOJ502 0.0 0.8 1.0
C11 A:AOJ502 1.3 0.1 1.0
C8 A:AOJ502 2.4 0.1 1.0
C10 A:AOJ502 2.4 0.2 1.0
C A:GLY262 2.8 88.1 1.0
CA A:GLY262 3.1 88.4 1.0
O A:GLY262 3.1 88.1 1.0
N A:SER263 3.2 88.0 1.0
CD2 A:LEU234 3.6 83.1 1.0
C9 A:AOJ502 3.6 0.0 1.0
C7 A:AOJ502 3.6 0.6 1.0
CB A:LEU234 3.7 83.0 1.0
CA A:SER263 4.0 87.7 1.0
CG A:LEU234 4.0 83.0 1.0
OG1 A:THR379 4.1 0.3 1.0
N A:GLY262 4.1 88.2 1.0
CD1 A:LEU234 4.1 83.0 1.0
C6 A:AOJ502 4.2 0.5 1.0
SG A:CYS129 4.4 76.0 1.0
CB A:THR379 4.5 0.9 1.0
O A:LEU234 4.6 84.2 1.0
C A:SER263 4.7 86.0 1.0
CA A:LEU234 4.8 84.2 1.0
CG2 A:THR379 4.9 0.2 1.0
CE2 A:PHE163 4.9 86.5 1.0
C12 A:AOJ502 5.0 0.7 1.0

Fluorine binding site 2 out of 3 in 6pz1

Go back to Fluorine Binding Sites List in 6pz1
Fluorine binding site 2 out of 3 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si 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 Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:72.5
occ:1.00
 F1 B:AOJ502 0.0 72.5 1.0
C11 B:AOJ502 1.3 72.3 1.0
C8 B:AOJ502 2.4 72.2 1.0
C10 B:AOJ502 2.4 71.6 1.0
C B:GLY262 3.1 79.1 1.0
CA B:GLY262 3.1 78.9 1.0
O B:GLY262 3.3 79.9 1.0
CD2 B:LEU234 3.5 68.6 1.0
C9 B:AOJ502 3.6 71.3 1.0
C7 B:AOJ502 3.7 71.3 1.0
CD1 B:LEU234 3.7 67.9 1.0
N B:SER263 3.7 78.5 1.0
CB B:LEU234 3.7 67.8 1.0
CG B:LEU234 3.8 68.2 1.0
N B:GLY262 4.1 78.7 1.0
C6 B:AOJ502 4.2 71.0 1.0
OG1 B:THR379 4.3 88.1 1.0
SG B:CYS129 4.3 64.3 1.0
CA B:SER263 4.4 78.0 1.0
CB B:THR379 4.6 88.2 1.0
O B:LEU234 4.7 66.1 1.0
CA B:LEU234 4.8 67.8 1.0
C B:SER263 5.0 77.2 1.0

Fluorine binding site 3 out of 3 in 6pz1

Go back to Fluorine Binding Sites List in 6pz1
Fluorine binding site 3 out of 3 in the Crystal Structure of Human Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si 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 Indoleamine 2,3-Dioxygenase 1 in Complex with Pf-06840003 in Active Site and Si Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:0.3
occ:1.00
 F1 B:AOJ503 0.0 0.3 1.0
C11 B:AOJ503 1.3 0.0 1.0
C8 B:AOJ503 2.4 0.7 1.0
C10 B:AOJ503 2.4 0.1 1.0
CG1 B:VAL170 2.9 71.4 1.0
CB B:ALA210 3.4 96.9 1.0
O B:VAL170 3.6 71.9 1.0
C9 B:AOJ503 3.6 0.1 1.0
CE1 B:PHE270 3.6 98.6 1.0
C7 B:AOJ503 3.7 0.7 1.0
CD1 B:PHE270 3.9 98.0 1.0
CB B:ALA174 4.1 79.0 1.0
C6 B:AOJ503 4.2 0.2 1.0
CD1 B:LEU342 4.2 80.4 1.0
C B:VAL170 4.3 71.7 1.0
CB B:VAL170 4.3 71.4 1.0
CA B:ALA210 4.6 96.9 1.0
O2 B:AOJ503 4.7 0.1 1.0
CA B:VAL170 4.7 71.2 1.0
CZ B:PHE270 4.7 99.0 1.0
CD2 B:LEU342 4.7 80.6 1.0
O B:ALA210 4.8 96.7 1.0
C B:ALA210 4.9 97.0 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 00:32:44 2024

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