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Magnesium in PDB 6wo8: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion, PDB code: 6wo8 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) 43.01 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.28, 59.48, 62.26, 90, 90, 90
R / Rfree (%) 14.9 / 21.6

Other elements in 6wo8:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion (pdb code 6wo8). 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion, PDB code: 6wo8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wo8

Go back to Magnesium Binding Sites List in 6wo8
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.9
occ:1.00
 O55 A:U6J401 2.0 20.8 1.0
O44 A:U6J401 2.0 23.6 1.0
O A:GLY50 2.0 15.7 1.0
OE1 A:GLU70 2.0 27.6 1.0
O35 A:U6J401 2.0 19.2 1.0
O A:HOH506 2.1 26.8 1.0
CD A:GLU70 3.0 20.1 1.0
PA5 A:U6J401 3.2 15.2 1.0
C A:GLY50 3.2 14.7 1.0
MG A:MG403 3.2 26.1 1.0
PA4 A:U6J401 3.3 16.0 1.0
OE2 A:GLU70 3.3 18.9 1.0
PB5 A:U6J401 3.3 17.2 1.0
O45 A:U6J401 3.5 17.8 1.0
O14 A:U6J401 3.5 18.2 1.0
CA A:GLY51 3.6 15.1 1.0
O A:HOH578 3.7 21.4 1.0
O24 A:U6J401 3.8 17.2 1.0
N A:GLY51 3.9 15.3 1.0
O15 A:U6J401 3.9 17.0 1.0
OE2 A:GLU66 4.1 18.5 1.0
O75 A:U6J401 4.2 19.6 1.0
NH1 A:ARG20 4.2 21.6 1.0
O A:HOH547 4.3 28.0 1.0
CA A:GLY50 4.4 16.0 1.0
CG A:GLU70 4.4 18.8 1.0
O25 A:U6J401 4.4 19.3 1.0
N A:GLY50 4.5 14.8 1.0
O65 A:U6J401 4.5 18.0 1.0
O34 A:U6J401 4.5 15.6 1.0
NH2 A:ARG115 4.6 23.1 1.0
C4 A:U6J401 4.7 17.3 1.0
F A:F407 4.7 23.2 1.0
C5 A:U6J401 4.7 19.0 1.0
O A:HOH532 4.9 38.0 1.0
CD A:GLU66 4.9 22.4 1.0

Magnesium binding site 2 out of 3 in 6wo8

Go back to Magnesium Binding Sites List in 6wo8
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:26.1
occ:1.00
 F A:F407 2.0 23.2 1.0
O A:HOH563 2.1 32.7 1.0
O55 A:U6J401 2.1 20.8 1.0
OE1 A:GLU70 2.2 27.6 1.0
O A:HOH578 2.2 21.4 1.0
OE2 A:GLU66 2.2 18.5 1.0
PB5 A:U6J401 3.1 17.2 1.0
CD A:GLU70 3.2 20.1 1.0
MG A:MG402 3.2 17.9 1.0
CD A:GLU66 3.2 22.4 1.0
CG A:GLU70 3.5 18.8 1.0
OE1 A:GLU66 3.5 27.7 1.0
MG A:MG404 3.6 25.1 1.0
O65 A:U6J401 3.6 18.0 1.0
O44 A:U6J401 3.6 23.6 1.0
O75 A:U6J401 3.7 19.6 1.0
O A:HOH644 3.8 34.9 1.0
O A:HOH505 3.8 42.9 1.0
O A:GLY50 4.0 15.7 1.0
O A:HOH554 4.2 29.8 1.0
OE2 A:GLU69 4.2 19.6 1.0
O A:HOH540 4.3 26.2 1.0
O A:HOH590 4.3 32.2 1.0
OE2 A:GLU70 4.3 18.9 1.0
O45 A:U6J401 4.5 17.8 1.0
CA A:GLY51 4.5 15.1 1.0
CG A:GLU66 4.5 21.4 1.0
C A:GLY50 4.7 14.7 1.0
O35 A:U6J401 4.8 19.2 1.0
NH2 A:ARG115 4.8 23.1 1.0
O A:HOH506 4.8 26.8 1.0
CB A:GLU66 4.9 20.4 1.0
N A:GLY51 5.0 15.3 1.0
OD2 A:ASP109 5.0 23.4 1.0
CB A:GLU70 5.0 17.9 1.0

Magnesium binding site 3 out of 3 in 6wo8

Go back to Magnesium Binding Sites List in 6wo8
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:25.1
occ:1.00
 F A:F407 1.8 23.2 1.0
O A:HOH554 2.0 29.8 1.0
O65 A:U6J401 2.0 18.0 1.0
O A:HOH530 2.1 26.0 1.0
O A:HOH611 2.2 32.2 1.0
OE1 A:GLU66 2.2 27.7 1.0
PB5 A:U6J401 3.1 17.2 1.0
CD A:GLU66 3.2 22.4 1.0
OE2 A:GLU66 3.6 18.5 1.0
MG A:MG403 3.6 26.1 1.0
O75 A:U6J401 3.7 19.6 1.0
O55 A:U6J401 3.8 20.8 1.0
O A:HOH634 3.9 44.5 1.0
O A:HOH568 4.0 32.9 1.0
NH1 A:ARG65 4.0 17.6 1.0
O A:HOH644 4.1 34.9 1.0
O A:HOH520 4.1 38.5 1.0
O A:HOH505 4.1 42.9 1.0
N A:GLY52 4.2 18.3 1.0
OE2 A:GLU69 4.2 19.6 1.0
O A:GLY52 4.3 20.2 1.0
O A:HOH563 4.4 32.7 1.0
O45 A:U6J401 4.5 17.8 1.0
CG A:GLU66 4.5 21.4 1.0
OE2 A:GLU54 4.6 44.3 1.0
O A:HOH572 4.7 47.9 1.0
CA A:GLY51 4.8 15.1 1.0
O A:HOH578 4.8 21.4 1.0
CA A:GLY52 4.9 19.1 1.0
C A:GLY51 4.9 15.3 1.0
NH2 A:ARG65 4.9 20.6 1.0
CZ A:ARG65 4.9 17.7 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: Tue Oct 1 23:03:32 2024

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