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Fluorine in PDB 8tf9: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi, PDB code: 8tf9 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) 35.94 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.995, 59.597, 62.695, 90, 90, 90
R / Rfree (%) 16.1 / 18.8

Other elements in 8tf9:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi (pdb code 8tf9). 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-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi, PDB code: 8tf9:

Fluorine binding site 1 out of 1 in 8tf9

Go back to Fluorine Binding Sites List in 8tf9
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi


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-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:21.0
occ:1.00
 MG A:MG404 1.9 18.5 1.0
MG A:MG403 2.0 18.0 1.0
O A:HOH505 2.3 19.9 1.0
PB5 A:I7P401 2.6 20.7 1.0
O65 A:I7P401 2.7 17.6 1.0
O55 A:I7P401 2.8 15.2 1.0
O A:HOH551 2.8 20.9 1.0
O75 A:I7P401 2.9 22.7 1.0
O A:HOH587 2.9 18.8 1.0
O A:HOH616 2.9 20.1 1.0
O A:HOH539 2.9 19.6 1.0
OE1 A:GLU66 3.0 17.5 1.0
OE2 A:GLU66 3.1 16.5 1.0
O A:HOH657 3.3 30.3 1.0
CD A:GLU66 3.4 17.8 1.0
O A:HOH638 3.7 37.6 1.0
OE2 A:GLU69 3.8 20.0 1.0
O A:HOH651 3.9 34.6 1.0
O A:HOH572 4.0 20.3 1.0
OE1 A:GLU70 4.1 16.6 1.0
O45 A:I7P401 4.3 18.8 1.0
O A:HOH561 4.4 23.1 1.0
MG A:MG402 4.6 16.9 1.0
O A:HOH639 4.6 36.3 1.0
O44 A:I7P401 4.8 18.5 1.0
O A:HOH509 4.9 39.2 1.0
O A:HOH605 4.9 26.6 1.0
CG A:GLU66 4.9 16.2 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 08:37:26 2025

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