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Magnesium in PDB 6wof: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride., PDB code: 6wof was solved by G.N.Zong, H.C.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.79 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.062, 59.827, 62.729, 90, 90, 90
R / Rfree (%) 12.3 / 14.8

Other elements in 6wof:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. (pdb code 6wof). 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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride., PDB code: 6wof:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wof

Go back to Magnesium Binding Sites List in 6wof
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.


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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.9
occ:1.00
 O24 A:IHP506 2.1 12.8 1.0
O A:HOH612 2.1 12.8 1.0
O25 A:IHP506 2.1 14.0 1.0
OE1 A:GLU70 2.1 11.1 1.0
O A:HOH614 2.1 10.6 1.0
O A:GLY50 2.1 9.8 1.0
CD A:GLU70 3.0 11.6 1.0
MG A:MG502 3.2 32.7 1.0
C A:GLY50 3.3 9.1 1.0
P5 A:IHP506 3.3 18.5 1.0
OE2 A:GLU70 3.3 11.2 1.0
P4 A:IHP506 3.3 18.2 1.0
O34 A:IHP506 3.6 20.6 1.0
O15 A:IHP506 3.6 22.9 1.0
CA A:GLY51 3.7 10.1 1.0
O35 A:IHP506 3.7 20.0 1.0
O A:HOH680 3.8 40.2 1.0
MG A:MG503 3.8 28.8 1.0
N A:GLY51 3.9 9.4 1.0
O14 A:IHP506 4.0 23.9 1.0
OE2 A:GLU66 4.0 15.6 1.0
NH1 A:ARG20 4.1 10.7 1.0
O A:HOH695 4.2 30.7 1.0
O A:HOH649 4.4 15.0 1.0
CG A:GLU70 4.4 11.7 1.0
N A:GLY50 4.4 8.7 1.0
CA A:GLY50 4.5 9.1 1.0
O45 A:IHP506 4.5 21.2 1.0
O44 A:IHP506 4.5 16.9 1.0
NH2 A:ARG115 4.7 24.4 1.0
C5 A:IHP506 4.7 21.7 1.0
C4 A:IHP506 4.8 24.8 1.0
O A:HOH736 4.8 36.9 1.0
CD A:GLU66 5.0 14.8 1.0
O A:HOH602 5.0 23.2 1.0

Magnesium binding site 2 out of 3 in 6wof

Go back to Magnesium Binding Sites List in 6wof
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.


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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.7
occ:1.00
 O A:HOH612 1.9 12.8 1.0
O A:HOH619 2.0 29.8 1.0
O A:HOH680 2.1 40.2 1.0
O A:HOH736 2.2 36.9 1.0
OE1 A:GLU70 2.3 11.1 1.0
OE2 A:GLU66 2.3 15.6 1.0
MG A:MG503 3.0 28.8 1.0
MG A:MG501 3.2 11.9 1.0
CD A:GLU70 3.2 11.6 1.0
CD A:GLU66 3.4 14.8 1.0
CG A:GLU70 3.5 11.7 1.0
O25 A:IHP506 3.6 14.0 1.0
O A:HOH601 3.6 31.9 1.0
OE1 A:GLU66 3.7 16.8 1.0
O A:GLY50 3.9 9.8 1.0
O A:HOH695 4.0 30.7 1.0
O A:HOH640 4.1 27.0 1.0
OE2 A:GLU69 4.2 27.2 1.0
O A:HOH602 4.3 23.2 1.0
O34 A:IHP506 4.3 20.6 1.0
OE2 A:GLU70 4.4 11.2 1.0
O A:HOH658 4.4 32.5 1.0
CA A:GLY51 4.6 10.1 1.0
O24 A:IHP506 4.7 12.8 1.0
CG A:GLU66 4.7 14.0 1.0
OD2 A:ASP109 4.7 16.5 1.0
C A:GLY50 4.7 9.1 1.0
NH2 A:ARG115 4.8 24.4 1.0
O A:HOH614 4.8 10.6 1.0

Magnesium binding site 3 out of 3 in 6wof

Go back to Magnesium Binding Sites List in 6wof
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride.


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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:28.8
occ:1.00
 O A:HOH612 2.1 12.8 1.0
O34 A:IHP506 2.1 20.6 1.0
O A:HOH602 2.2 23.2 1.0
O A:HOH695 2.2 30.7 1.0
O A:HOH650 2.2 35.9 1.0
O A:HOH736 2.4 36.9 1.0
O A:HOH601 2.9 31.9 1.0
MG A:MG502 3.0 32.7 1.0
P4 A:IHP506 3.5 18.2 1.0
O A:HOH680 3.5 40.2 1.0
O25 A:IHP506 3.7 14.0 1.0
MG A:MG501 3.8 11.9 1.0
O A:HOH672 3.9 32.6 1.0
O14 A:IHP506 3.9 23.9 1.0
O24 A:IHP506 4.0 12.8 1.0
O A:HOH613 4.0 46.7 1.0
OE1 A:GLU66 4.2 16.8 1.0
OE2 A:GLU66 4.2 15.6 1.0
N A:GLY52 4.4 11.6 1.0
CA A:GLY51 4.4 10.1 1.0
O A:HOH615 4.5 28.5 1.0
OE1 A:GLU70 4.5 11.1 1.0
O A:HOH730 4.5 57.3 1.0
O A:HOH658 4.6 32.5 1.0
CD A:GLU66 4.6 14.8 1.0
O A:HOH619 4.6 29.8 1.0
O44 A:IHP506 4.7 16.9 1.0
C A:GLY51 5.0 10.1 1.0

Reference:

G.Zong, N.Jork, S.Hostachy, D.Fiedler, H.J.Jessen, S.B.Shears, H.Wang. New Structural Insights Reveal An Expanded Reaction Cycle For Inositol Pyrophosphate Hydrolysis By Human DIPP1. Faseb J. V. 35 21275 2021.
ISSN: ESSN 1530-6860
PubMed: 33475202
DOI: 10.1096/FJ.202001489R
Page generated: Wed Aug 13 19:51:25 2025

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