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Fluorine in PDB 8tfa: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa was solved by G.Zong, H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.304, 59.64, 62.698, 90, 90, 90
R / Rfree (%) 15.4 / 16.9

Other elements in 8tfa:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk (pdb code 8tfa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa:

Fluorine binding site 1 out of 1 in 8tfa

Go back to Fluorine Binding Sites List in 8tfa
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:22.8
occ:1.00
 MG A:MG404 2.0 20.2 1.0
MG A:MG403 2.0 18.9 1.0
O A:HOH504 2.3 23.8 1.0
O65 A:U6J401 2.7 18.8 1.0
PB5 A:U6J401 2.8 20.3 1.0
O55 A:U6J401 2.8 18.0 1.0
O A:HOH565 2.8 22.4 1.0
O A:HOH573 2.8 21.1 1.0
O A:HOH560 2.8 19.9 1.0
O A:HOH631 2.9 22.3 1.0
OE2 A:GLU66 3.0 18.7 1.0
O75 A:U6J401 3.0 23.0 1.0
OE1 A:GLU66 3.0 20.7 1.0
O A:HOH670 3.1 33.0 1.0
CD A:GLU66 3.4 20.4 1.0
OE2 A:GLU69 3.7 22.9 1.0
O A:HOH648 3.8 44.3 1.0
O A:HOH638 3.9 36.0 1.0
O A:HOH575 4.0 22.4 1.0
OE1 A:GLU70 4.1 18.8 1.0
O A:HOH542 4.3 25.7 1.0
O45 A:U6J401 4.4 19.5 1.0
O A:HOH651 4.5 41.9 1.0
MG A:MG402 4.6 18.6 1.0
O44 A:U6J401 4.9 19.7 1.0
CG A:GLU66 4.9 18.3 1.0
O A:HOH620 4.9 29.5 1.0
CD A:GLU69 4.9 23.3 1.0

Reference:

G.Zong, H.Wang, S.B.Shears. Biochemical and Structural Characterization of A Giant Virus Inositol Pyrophosphate Kinase Embo J. 2023.
ISSN: ESSN 1460-2075
Page generated: Wed Jul 16 08:37:27 2025

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