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Magnesium 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:

Chlorine (Cl) 2 atoms
Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where 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:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8tf9

Go back to Magnesium Binding Sites List in 8tf9
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg402

b:16.9
occ:1.00
 O55 A:I7P401 2.0 15.2 1.0
O35 A:I7P401 2.0 17.4 1.0
O44 A:I7P401 2.1 18.5 1.0
OE1 A:GLU70 2.1 16.6 1.0
O A:HOH527 2.1 17.0 1.0
O A:GLY50 2.1 15.0 1.0
CD A:GLU70 3.0 17.7 1.0
PA5 A:I7P401 3.2 17.8 1.0
MG A:MG403 3.2 18.0 1.0
PA4 A:I7P401 3.3 20.3 1.0
OE2 A:GLU70 3.3 17.1 1.0
C A:GLY50 3.3 16.1 1.0
PB5 A:I7P401 3.4 20.7 1.0
O45 A:I7P401 3.5 18.8 1.0
O14 A:I7P401 3.6 31.0 1.0
O24 A:I7P401 3.6 20.6 1.0
O A:HOH587 3.6 18.8 1.0
CA A:GLY51 3.7 17.9 1.0
O15 A:I7P401 3.9 19.8 1.0
N A:GLY51 4.0 16.6 1.0
OE2 A:GLU66 4.0 16.5 1.0
O75 A:I7P401 4.1 22.7 1.0
NH1 A:ARG20 4.1 16.0 1.0
O A:HOH548 4.2 17.3 1.0
N A:GLY50 4.4 15.5 1.0
CG A:GLU70 4.4 17.3 1.0
CA A:GLY50 4.5 16.5 1.0
O25 A:I7P401 4.5 19.6 1.0
O34 A:I7P401 4.5 27.2 1.0
C4 A:I7P401 4.6 26.6 1.0
F A:F407 4.6 21.0 1.0
O65 A:I7P401 4.6 17.6 1.0
C5 A:I7P401 4.6 24.7 1.0
NH2 A:ARG115 4.8 22.9 1.0
O A:HOH509 4.8 39.2 1.0
CD A:GLU66 4.9 17.8 1.0

Magnesium binding site 2 out of 3 in 8tf9

Go back to Magnesium Binding Sites List in 8tf9
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg403

b:18.0
occ:1.00
 F A:F407 2.0 21.0 1.0
O A:HOH539 2.1 19.6 1.0
OE2 A:GLU66 2.1 16.5 1.0
O55 A:I7P401 2.1 15.2 1.0
O A:HOH587 2.1 18.8 1.0
OE1 A:GLU70 2.2 16.6 1.0
CD A:GLU66 3.1 17.8 1.0
PB5 A:I7P401 3.1 20.7 1.0
CD A:GLU70 3.2 17.7 1.0
MG A:MG402 3.2 16.9 1.0
O A:HOH505 3.4 19.9 1.0
OE1 A:GLU66 3.4 17.5 1.0
CG A:GLU70 3.5 17.3 1.0
MG A:MG404 3.5 18.5 1.0
O75 A:I7P401 3.6 22.7 1.0
O44 A:I7P401 3.7 18.5 1.0
O65 A:I7P401 3.7 17.6 1.0
OE2 A:GLU69 3.9 20.0 1.0
O A:GLY50 4.1 15.0 1.0
O A:HOH657 4.2 30.3 1.0
O A:HOH551 4.3 20.9 1.0
OE2 A:GLU70 4.3 17.1 1.0
O A:HOH561 4.3 23.1 1.0
O A:HOH605 4.4 26.6 1.0
CG A:GLU66 4.4 16.2 1.0
CA A:GLY51 4.5 17.9 1.0
O45 A:I7P401 4.6 18.8 1.0
CB A:GLU66 4.7 16.9 1.0
C A:GLY50 4.8 16.1 1.0
O35 A:I7P401 4.8 17.4 1.0
O A:HOH616 4.9 20.1 1.0
O A:HOH527 4.9 17.0 1.0

Magnesium binding site 3 out of 3 in 8tf9

Go back to Magnesium Binding Sites List in 8tf9
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg404

b:18.5
occ:1.00
 F A:F407 1.9 21.0 1.0
OE1 A:GLU66 2.0 17.5 1.0
O65 A:I7P401 2.1 17.6 1.0
O A:HOH572 2.1 20.3 1.0
O A:HOH551 2.1 20.9 1.0
O A:HOH616 2.1 20.1 1.0
CD A:GLU66 3.1 17.8 1.0
PB5 A:I7P401 3.1 20.7 1.0
OE2 A:GLU66 3.5 16.5 1.0
MG A:MG403 3.5 18.0 1.0
O55 A:I7P401 3.7 15.2 1.0
O A:HOH505 3.8 19.9 1.0
O75 A:I7P401 3.8 22.7 1.0
NH1 A:ARG65 4.0 18.4 1.0
OE2 A:GLU69 4.0 20.0 1.0
N A:GLY52 4.1 16.2 1.0
O A:HOH651 4.1 34.6 1.0
O A:HOH611 4.1 31.8 1.0
O A:HOH638 4.1 37.6 1.0
O A:HOH539 4.3 19.6 1.0
O A:GLY52 4.3 17.9 1.0
CG A:GLU66 4.4 16.2 1.0
OE2 A:GLU54 4.5 34.9 1.0
O45 A:I7P401 4.5 18.8 1.0
O A:HOH657 4.7 30.3 1.0
O A:HOH587 4.8 18.8 1.0
CA A:GLY51 4.8 17.9 1.0
C A:GLY51 4.8 16.1 1.0
CA A:GLY52 4.8 16.7 1.0
NH2 A:ARG65 4.8 19.3 1.0
CZ A:ARG65 4.9 19.0 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: Fri Aug 15 16:20:36 2025

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