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Magnesium in PDB 8tfa: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa was solved by G.Zong, H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.304, 59.64, 62.698, 90, 90, 90
R / Rfree (%) 15.4 / 16.9

Other elements in 8tfa:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk 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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk (pdb code 8tfa). 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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.6
occ:1.00
 O55 A:U6J401 2.0 18.0 1.0
O35 A:U6J401 2.1 18.6 1.0
O44 A:U6J401 2.1 19.7 1.0
OE1 A:GLU70 2.1 18.8 1.0
O A:GLY50 2.1 17.8 1.0
O A:HOH529 2.1 18.9 1.0
CD A:GLU70 3.0 19.0 1.0
MG A:MG403 3.2 18.9 1.0
PA5 A:U6J401 3.2 18.9 1.0
PA4 A:U6J401 3.3 19.8 1.0
OE2 A:GLU70 3.3 18.4 1.0
C A:GLY50 3.3 17.2 1.0
PB5 A:U6J401 3.4 20.3 1.0
O45 A:U6J401 3.5 19.5 1.0
O A:HOH573 3.6 21.1 1.0
O14 A:U6J401 3.6 21.0 1.0
CA A:GLY51 3.7 17.1 1.0
O24 A:U6J401 3.7 20.1 1.0
O15 A:U6J401 3.9 19.4 1.0
N A:GLY51 4.0 17.3 1.0
OE2 A:GLU66 4.0 18.7 1.0
O75 A:U6J401 4.1 23.0 1.0
NH1 A:ARG20 4.1 18.0 1.0
O A:HOH534 4.3 23.3 1.0
N A:GLY50 4.4 17.7 1.0
CG A:GLU70 4.4 18.8 1.0
O65 A:U6J401 4.5 18.8 1.0
CA A:GLY50 4.5 18.0 1.0
O25 A:U6J401 4.5 20.3 1.0
O34 A:U6J401 4.5 23.2 1.0
F A:F406 4.6 22.8 1.0
NH2 A:ARG115 4.7 24.3 1.0
C5 A:U6J401 4.7 22.1 1.0
C4 A:U6J401 4.7 23.5 1.0
CD A:GLU66 4.8 20.4 1.0

Magnesium binding site 2 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:18.9
occ:1.00
 F A:F406 2.0 22.8 1.0
OE2 A:GLU66 2.0 18.7 1.0
O A:HOH560 2.1 19.9 1.0
O55 A:U6J401 2.1 18.0 1.0
O A:HOH573 2.1 21.1 1.0
OE1 A:GLU70 2.1 18.8 1.0
CD A:GLU66 3.1 20.4 1.0
PB5 A:U6J401 3.1 20.3 1.0
CD A:GLU70 3.1 19.0 1.0
MG A:MG402 3.2 18.6 1.0
OE1 A:GLU66 3.5 20.7 1.0
CG A:GLU70 3.5 18.8 1.0
MG A:MG404 3.5 20.2 1.0
O A:HOH504 3.5 23.8 1.0
O65 A:U6J401 3.6 18.8 1.0
O75 A:U6J401 3.7 23.0 1.0
O44 A:U6J401 3.8 19.7 1.0
OE2 A:GLU69 4.0 22.9 1.0
O A:GLY50 4.0 17.8 1.0
O A:HOH670 4.2 33.0 1.0
OE2 A:GLU70 4.3 18.4 1.0
O A:HOH565 4.3 22.4 1.0
O A:HOH542 4.3 25.7 1.0
CG A:GLU66 4.4 18.3 1.0
O A:HOH620 4.5 29.5 1.0
O45 A:U6J401 4.5 19.5 1.0
CA A:GLY51 4.5 17.1 1.0
CB A:GLU66 4.8 18.2 1.0
C A:GLY50 4.8 17.2 1.0
O35 A:U6J401 4.8 18.6 1.0
O A:HOH631 4.9 22.3 1.0
NH2 A:ARG115 4.9 24.3 1.0
O A:HOH529 4.9 18.9 1.0
CB A:GLU70 5.0 17.8 1.0

Magnesium binding site 3 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:20.2
occ:1.00
 F A:F406 2.0 22.8 1.0
O65 A:U6J401 2.1 18.8 1.0
OE1 A:GLU66 2.1 20.7 1.0
O A:HOH575 2.1 22.4 1.0
O A:HOH565 2.1 22.4 1.0
O A:HOH631 2.1 22.3 1.0
CD A:GLU66 3.1 20.4 1.0
PB5 A:U6J401 3.1 20.3 1.0
OE2 A:GLU66 3.4 18.7 1.0
MG A:MG403 3.5 18.9 1.0
O A:HOH504 3.7 23.8 1.0
O55 A:U6J401 3.7 18.0 1.0
O75 A:U6J401 3.8 23.0 1.0
NH1 A:ARG65 4.0 20.3 1.0
OE2 A:GLU69 4.0 22.9 1.0
N A:GLY52 4.1 18.0 1.0
O A:HOH584 4.1 27.6 1.0
O A:HOH648 4.1 44.3 1.0
O A:HOH638 4.2 36.0 1.0
O A:HOH502 4.3 41.2 1.0
O A:HOH560 4.3 19.9 1.0
O A:GLY52 4.3 20.0 1.0
CG A:GLU66 4.4 18.3 1.0
O45 A:U6J401 4.5 19.5 1.0
O A:HOH670 4.5 33.0 1.0
O A:HOH573 4.7 21.1 1.0
CA A:GLY51 4.8 17.1 1.0
CA A:GLY52 4.8 18.8 1.0
C A:GLY51 4.8 18.0 1.0
NH2 A:ARG65 4.9 20.4 1.0
CZ A:ARG65 4.9 19.2 1.0

Reference:

G.Zong, H.Wang, S.B.Shears. Biochemical and Structural Characterization of A Giant Virus Inositol Pyrophosphate Kinase Embo J. 2023.
ISSN: ESSN 1460-2075
Page generated: Thu Dec 28 10:27:01 2023

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