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

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

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

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride., PDB code: 6woc 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) 31.40 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.708, 59.611, 62.581, 90, 90, 90
R / Rfree (%) 13.8 / 16.4

Other elements in 6woc:

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

Magnesium binding site 1 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN 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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.8
occ:1.00
 O35 A:I7P401 2.0 11.8 1.0
O44 A:I7P401 2.1 13.6 1.0
OE1 A:GLU70 2.1 12.4 1.0
O A:HOH523 2.1 10.9 1.0
O55 A:I7P401 2.1 13.9 1.0
O A:GLY50 2.1 11.1 1.0
CD A:GLU70 3.0 11.4 1.0
PA5 A:I7P401 3.2 13.0 1.0
PA4 A:I7P401 3.2 13.7 1.0
MG A:MG403 3.3 33.3 1.0
C A:GLY50 3.3 10.0 1.0
PB5 A:I7P401 3.3 18.9 1.0
OE2 A:GLU70 3.4 11.7 1.0
O45 A:I7P401 3.5 15.8 1.0
O14 A:I7P401 3.6 15.8 1.0
O24 A:I7P401 3.7 15.8 1.0
CA A:GLY51 3.7 10.3 1.0
O A:HOH614 3.8 43.1 1.0
O15 A:I7P401 3.9 15.7 1.0
N A:GLY51 4.0 9.8 1.0
OE2 A:GLU66 4.1 16.8 1.0
O75 A:I7P401 4.1 22.4 1.0
NH2 A:ARG20 4.2 15.3 1.0
CG A:GLU70 4.4 11.7 1.0
O A:HOH539 4.4 16.3 1.0
O25 A:I7P401 4.5 12.4 1.0
N A:GLY50 4.5 9.9 1.0
O34 A:I7P401 4.5 17.3 1.0
CA A:GLY50 4.5 10.1 1.0
O65 A:I7P401 4.5 21.3 1.0
NH2 A:ARG115 4.6 18.5 1.0
C5 A:I7P401 4.7 17.0 1.0
C4 A:I7P401 4.7 16.4 1.0

Magnesium binding site 2 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN 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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:33.3
occ:1.00
 O55 A:I7P401 2.1 13.9 1.0
O A:HOH509 2.1 28.1 1.0
O A:HOH625 2.3 38.8 1.0
OE1 A:GLU70 2.3 12.4 1.0
O A:HOH614 2.4 43.1 1.0
OE2 A:GLU66 2.4 16.8 1.0
PB5 A:I7P401 3.2 18.9 1.0
CD A:GLU70 3.2 11.4 1.0
MG A:MG402 3.3 10.8 1.0
CD A:GLU66 3.4 14.9 1.0
CG A:GLU70 3.4 11.7 1.0
MG A:MG404 3.7 30.1 1.0
O75 A:I7P401 3.7 22.4 1.0
O65 A:I7P401 3.8 21.3 1.0
OE1 A:GLU66 3.8 18.2 1.0
O44 A:I7P401 3.8 13.6 1.0
OE2 A:GLU69 3.9 26.2 1.0
O A:HOH551 4.0 30.0 1.0
O A:GLY50 4.1 11.1 1.0
O A:HOH550 4.2 34.1 1.0
OE2 A:GLU70 4.4 11.7 1.0
O45 A:I7P401 4.5 15.8 1.0
OD2 A:ASP109 4.7 17.0 1.0
CA A:GLY51 4.7 10.3 1.0
CG A:GLU66 4.7 13.8 1.0
NH2 A:ARG115 4.8 18.5 1.0
C A:GLY50 4.8 10.0 1.0
O35 A:I7P401 4.8 11.8 1.0
CB A:GLU70 4.9 11.7 1.0
O A:HOH523 5.0 10.9 1.0
CB A:GLU69 5.0 15.9 1.0

Magnesium binding site 3 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN 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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.1
occ:1.00
 O A:HOH550 1.9 34.1 1.0
O A:HOH548 2.0 22.2 1.0
O65 A:I7P401 2.0 21.3 1.0
O A:HOH625 2.3 38.8 1.0
OE1 A:GLU66 2.3 18.2 1.0
O A:HOH631 2.5 38.4 1.0
PB5 A:I7P401 3.1 18.9 1.0
CD A:GLU66 3.3 14.9 1.0
OE2 A:GLU66 3.6 16.8 1.0
MG A:MG403 3.7 33.3 1.0
O55 A:I7P401 3.7 13.9 1.0
O A:HOH521 3.7 38.3 1.0
O75 A:I7P401 3.8 22.4 1.0
NH1 A:ARG65 3.9 15.1 1.0
OE2 A:GLU69 4.0 26.2 1.0
N A:GLY52 4.1 10.9 1.0
O A:HOH562 4.1 31.8 1.0
O A:GLY52 4.2 13.8 1.0
O45 A:I7P401 4.4 15.8 1.0
O A:HOH509 4.5 28.1 1.0
CG A:GLU66 4.6 13.8 1.0
CA A:GLY51 4.8 10.3 1.0
CA A:GLY52 4.8 10.7 1.0
C A:GLY51 4.8 9.5 1.0
NH2 A:ARG65 4.8 14.5 1.0
CZ A:ARG65 4.8 13.9 1.0
C A:GLY52 5.0 11.1 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: Sat Apr 3 16:39:24 2021

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