Magnesium in PDB 6wo7: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion

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

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion, PDB code: 6wo7 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) 43.13 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.365, 59.602, 62.493, 90, 90, 90
R / Rfree (%) 13.9 / 16.8

Other elements in 6wo7:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion 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 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion (pdb code 6wo7). 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 (5-IP7), Mg, and Fluoride Ion, PDB code: 6wo7:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wo7

Go back to Magnesium Binding Sites List in 6wo7
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion


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 (5-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:12.3
occ:1.00
 OE1 A:GLU70 2.1 11.8 1.0
O A:HOH532 2.1 9.9 1.0
O35 A:I7P401 2.1 12.4 1.0
O44 A:I7P401 2.2 12.1 1.0
O55 A:I7P401 2.2 11.1 1.0
O A:GLY50 2.2 10.2 1.0
CD A:GLU70 3.1 11.1 1.0
MG A:MG403 3.2 20.2 1.0
PA5 A:I7P401 3.2 12.1 1.0
PA4 A:I7P401 3.2 12.2 1.0
C A:GLY50 3.3 10.7 1.0
OE2 A:GLU70 3.4 10.7 1.0
PB5 A:I7P401 3.4 14.7 1.0
O45 A:I7P401 3.5 13.6 1.0
O14 A:I7P401 3.6 14.3 1.0
O A:HOH596 3.6 24.2 1.0
O24 A:I7P401 3.6 13.8 1.0
CA A:GLY51 3.7 10.8 1.0
O15 A:I7P401 3.9 12.8 1.0
O75 A:I7P401 4.0 17.2 1.0
N A:GLY51 4.0 10.8 1.0
OE2 A:GLU66 4.0 12.9 1.0
NH1 A:ARG20 4.1 12.9 1.0
O A:HOH556 4.4 14.7 1.0
CG A:GLU70 4.4 11.7 1.0
O65 A:I7P401 4.4 13.9 1.0
N A:GLY50 4.5 9.7 1.0
O34 A:I7P401 4.5 15.4 1.0
O25 A:I7P401 4.5 12.4 1.0
CA A:GLY50 4.5 10.1 1.0
NH2 A:ARG115 4.6 17.1 1.0
C5 A:I7P401 4.7 13.7 1.0
F A:F407 4.7 25.1 1.0
C4 A:I7P401 4.7 14.3 1.0
O A:HOH543 4.8 17.8 1.0
O A:HOH522 4.9 50.0 1.0
CD A:GLU66 5.0 12.1 1.0

Magnesium binding site 2 out of 3 in 6wo7

Go back to Magnesium Binding Sites List in 6wo7
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion


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 (5-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:20.2
occ:1.00
 O A:HOH543 1.8 17.8 1.0
O55 A:I7P401 2.1 11.1 1.0
F A:F407 2.1 25.1 1.0
OE2 A:GLU66 2.1 12.9 1.0
OE1 A:GLU70 2.2 11.8 1.0
O A:HOH596 2.2 24.2 1.0
PB5 A:I7P401 3.0 14.7 1.0
CD A:GLU66 3.2 12.1 1.0
CD A:GLU70 3.2 11.1 1.0
MG A:MG402 3.2 12.3 1.0
OE1 A:GLU66 3.5 13.8 1.0
CG A:GLU70 3.5 11.7 1.0
MG A:MG404 3.5 21.3 1.0
O65 A:I7P401 3.5 13.9 1.0
O75 A:I7P401 3.6 17.2 1.0
O A:HOH503 3.8 34.8 1.0
OE2 A:GLU69 3.9 18.2 1.0
O44 A:I7P401 3.9 12.1 1.0
O A:GLY50 4.0 10.2 1.0
O A:HOH542 4.0 21.7 1.0
O A:HOH590 4.2 31.9 1.0
O A:HOH653 4.3 37.8 1.0
OE2 A:GLU70 4.4 10.7 1.0
O A:HOH531 4.4 24.7 1.0
CA A:GLY51 4.4 10.8 1.0
O45 A:I7P401 4.4 13.6 1.0
CG A:GLU66 4.5 12.2 1.0
C A:GLY50 4.7 10.7 1.0
O35 A:I7P401 4.8 12.4 1.0
CB A:GLU66 4.8 11.5 1.0
NH2 A:ARG115 4.9 17.1 1.0
N A:GLY51 4.9 10.8 1.0
O A:HOH532 4.9 9.9 1.0
OD2 A:ASP109 5.0 15.5 1.0

Magnesium binding site 3 out of 3 in 6wo7

Go back to Magnesium Binding Sites List in 6wo7
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion


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 (5-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:21.3
occ:1.00
 O A:HOH542 1.9 21.7 1.0
F A:F407 2.0 25.1 1.0
O A:HOH557 2.0 16.8 1.0
O65 A:I7P401 2.1 13.9 1.0
OE1 A:GLU66 2.2 13.8 1.0
O A:HOH631 2.2 24.6 1.0
PB5 A:I7P401 3.1 14.7 1.0
CD A:GLU66 3.2 12.1 1.0
MG A:MG403 3.5 20.2 1.0
OE2 A:GLU66 3.6 12.9 1.0
O55 A:I7P401 3.6 11.1 1.0
O A:HOH506 3.6 34.4 1.0
O A:HOH503 3.7 34.8 1.0
O75 A:I7P401 3.8 17.2 1.0
O A:HOH563 3.9 22.6 1.0
NH1 A:ARG65 4.0 13.1 1.0
N A:GLY52 4.0 10.1 1.0
OE2 A:GLU69 4.0 18.2 1.0
O A:HOH543 4.1 17.8 1.0
O A:GLY52 4.2 12.6 1.0
O A:HOH650 4.2 42.7 1.0
O45 A:I7P401 4.5 13.6 1.0
CG A:GLU66 4.6 12.2 1.0
O A:HOH653 4.6 37.8 1.0
CA A:GLY51 4.7 10.8 1.0
CA A:GLY52 4.7 10.6 1.0
C A:GLY51 4.8 9.5 1.0
O A:HOH596 4.8 24.2 1.0
NH2 A:ARG65 4.8 12.7 1.0
O A:HOH636 4.8 49.3 1.0
CZ A:ARG65 4.8 12.2 1.0
C A:GLY52 5.0 10.8 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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