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Fluorine in PDB 8t98: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98 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) 36.49 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.103, 59.571, 62.43, 90, 90, 90
R / Rfree (%) 14.9 / 17.2

Other elements in 8t98:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion 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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion (pdb code 8t98). 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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98:

Fluorine binding site 1 out of 1 in 8t98

Go back to Fluorine Binding Sites List in 8t98
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion


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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:12.5
occ:1.00
 MG A:MG403 1.9 11.2 1.0
MG A:MG404 2.0 12.5 1.0
O A:HOH504 2.4 11.9 1.0
O65 A:U6J401 2.8 11.1 1.0
O A:HOH563 2.8 12.3 1.0
O A:HOH580 2.8 13.7 1.0
O55 A:U6J401 2.8 10.9 1.0
PB5 A:U6J401 2.9 11.1 1.0
O A:HOH581 2.9 12.6 1.0
OE2 A:GLU66 3.0 11.2 1.0
OE1 A:GLU66 3.0 12.1 1.0
O A:HOH659 3.0 15.1 1.0
O75 A:U6J401 3.1 12.5 1.0
O A:HOH699 3.3 25.4 1.0
CD A:GLU66 3.4 12.3 1.0
OE2 A:GLU69 3.6 15.2 1.0
O A:HOH531 3.8 26.8 1.0
O A:HOH536 3.9 27.0 1.0
O A:HOH583 4.0 14.2 1.0
OE1 A:GLU70 4.0 10.8 1.0
O A:HOH551 4.3 16.9 1.0
O45 A:U6J401 4.5 11.0 1.0
MG A:MG402 4.6 10.2 1.0
CD A:GLU69 4.8 15.0 1.0
O A:HOH689 4.8 27.6 1.0
CG A:GLU66 4.9 10.6 1.0
O24 A:U6J401 4.9 10.9 1.0
O A:HOH651 4.9 18.6 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 08:36:29 2025

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