Atomistry » Magnesium » PDB 6wj2-6wqx » 6woe
Atomistry »
  Magnesium »
    PDB 6wj2-6wqx »
      6woe »

Magnesium in PDB 6woe: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN 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 10MIN 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 10MIN 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 10MIN in the Absence of Fluoride., PDB code: 6woe 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) 31.60 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.265, 59.639, 62.693, 90, 90, 90
R / Rfree (%) 12.7 / 15.2

Other elements in 6woe:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN 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 10MIN in the Absence of Fluoride. (pdb code 6woe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN in the Absence of Fluoride., PDB code: 6woe:

Magnesium binding site 1 out of 1 in 6woe

Go back to Magnesium Binding Sites List in 6woe
Magnesium binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN 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 10MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.5
occ:1.00
 O25 A:IHP504 2.0 11.8 0.5
O24 A:IHP504 2.0 13.6 0.5
O24 A:IHP504 2.0 13.3 0.5
O A:HOH603 2.1 11.4 1.0
OE1 A:GLU70 2.1 12.0 1.0
O A:HOH643 2.1 13.3 1.0
O25 A:IHP504 2.1 13.4 0.5
O A:GLY50 2.2 10.8 1.0
CD A:GLU70 3.0 11.7 1.0
P5 A:IHP504 3.2 14.8 0.5
P5 A:IHP504 3.2 14.2 0.5
P4 A:IHP504 3.3 15.8 0.5
P4 A:IHP504 3.3 16.1 0.5
O35 A:IHP504 3.3 17.5 0.5
OE2 A:GLU70 3.3 11.8 1.0
C A:GLY50 3.3 9.7 1.0
O14 A:IHP504 3.5 20.4 0.5
O34 A:IHP504 3.5 16.6 0.5
O35 A:IHP504 3.6 17.5 0.5
CA A:GLY51 3.7 10.0 1.0
O15 A:IHP504 3.7 17.4 0.5
O15 A:IHP504 3.8 20.6 0.5
O34 A:IHP504 3.9 16.0 0.5
O14 A:IHP504 3.9 19.8 0.5
O A:HOH632 3.9 35.9 1.0
N A:GLY51 4.0 9.7 1.0
O A:HOH622 4.0 37.9 1.0
OE2 A:GLU66 4.1 18.2 1.0
NH1 A:ARG20 4.1 11.2 1.0
CG A:GLU70 4.4 12.4 1.0
O A:HOH659 4.4 16.6 1.0
O44 A:IHP504 4.4 19.4 0.5
O44 A:IHP504 4.4 15.9 0.5
O45 A:IHP504 4.5 11.1 0.5
N A:GLY50 4.5 9.6 1.0
O45 A:IHP504 4.5 14.4 0.5
CA A:GLY50 4.5 10.1 1.0
C5 A:IHP504 4.6 21.2 0.5
C4 A:IHP504 4.6 18.8 0.5
C4 A:IHP504 4.6 21.8 0.5
C5 A:IHP504 4.7 20.0 0.5
O A:HOH601 4.7 41.0 1.0
O A:HOH752 4.7 56.1 1.0
NH2 A:ARG115 4.8 23.2 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 19:51:11 2025

Last articles

Mg in 7DR0
Mg in 7DR1
Mg in 7DU2
Mg in 7DSP
Mg in 7DSJ
Mg in 7DSI
Mg in 7DRP
Mg in 7DSH
Mg in 7DSA
Mg in 7DRX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy