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Magnesium in PDB 8t98: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98 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) 36.49 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.103, 59.571, 62.43, 90, 90, 90
R / Rfree (%) 14.9 / 17.2

Other elements in 8t98:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, 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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion (pdb code 8t98). 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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.2
occ:1.00
 O55 A:U6J401 2.0 10.9 1.0
O35 A:U6J401 2.0 10.9 1.0
O24 A:U6J401 2.1 10.9 1.0
OE1 A:GLU70 2.1 10.8 1.0
O A:HOH532 2.1 11.0 1.0
O A:GLY50 2.1 9.6 1.0
CD A:GLU70 3.1 10.9 1.0
MG A:MG403 3.2 11.2 1.0
PA5 A:U6J401 3.2 11.0 1.0
PA4 A:U6J401 3.2 11.8 1.0
OE2 A:GLU70 3.3 10.3 1.0
C A:GLY50 3.3 9.5 1.0
PB5 A:U6J401 3.3 11.1 1.0
O45 A:U6J401 3.5 11.0 1.0
O A:HOH581 3.6 12.6 1.0
O14 A:U6J401 3.6 12.3 1.0
CA A:GLY51 3.7 9.8 1.0
O44 A:U6J401 3.7 12.0 1.0
O15 A:U6J401 3.9 11.9 1.0
OE2 A:GLU66 3.9 11.2 1.0
N A:GLY51 4.0 9.5 1.0
O75 A:U6J401 4.1 12.5 1.0
NH1 A:ARG20 4.2 10.4 1.0
O65 A:U6J401 4.4 11.1 1.0
N A:GLY50 4.4 10.1 1.0
CG A:GLU70 4.4 10.7 1.0
CA A:GLY50 4.5 10.1 1.0
O25 A:U6J401 4.5 11.9 1.0
O A:HOH552 4.5 18.0 1.0
O34 A:U6J401 4.5 14.0 1.0
NH2 A:ARG115 4.6 14.9 1.0
O A:HOH566 4.6 23.2 1.0
F A:F407 4.6 12.5 1.0
C5 A:U6J401 4.7 12.3 1.0
C4 A:U6J401 4.7 12.7 1.0
CD A:GLU66 4.8 12.3 1.0

Magnesium binding site 2 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.2
occ:1.00
 F A:F407 1.9 12.5 1.0
O A:HOH563 2.0 12.3 1.0
OE2 A:GLU66 2.1 11.2 1.0
O55 A:U6J401 2.1 10.9 1.0
OE1 A:GLU70 2.1 10.8 1.0
O A:HOH581 2.2 12.6 1.0
CD A:GLU66 3.1 12.3 1.0
PB5 A:U6J401 3.1 11.1 1.0
CD A:GLU70 3.2 10.9 1.0
MG A:MG402 3.2 10.2 1.0
OE1 A:GLU66 3.5 12.1 1.0
MG A:MG404 3.5 12.5 1.0
CG A:GLU70 3.5 10.7 1.0
O A:HOH504 3.5 11.9 1.0
O65 A:U6J401 3.6 11.1 1.0
O75 A:U6J401 3.7 12.5 1.0
O24 A:U6J401 3.7 10.9 1.0
OE2 A:GLU69 3.9 15.2 1.0
O A:GLY50 4.0 9.6 1.0
O A:HOH699 4.3 25.4 1.0
OE2 A:GLU70 4.3 10.3 1.0
O A:HOH580 4.3 13.7 1.0
O A:HOH551 4.4 16.9 1.0
CG A:GLU66 4.4 10.6 1.0
O A:HOH651 4.4 18.6 1.0
O45 A:U6J401 4.5 11.0 1.0
CA A:GLY51 4.5 9.8 1.0
CB A:GLU66 4.8 11.2 1.0
C A:GLY50 4.8 9.5 1.0
O35 A:U6J401 4.8 10.9 1.0
NH2 A:ARG115 4.9 14.9 1.0
O A:HOH659 4.9 15.1 1.0
O A:HOH532 4.9 11.0 1.0
CB A:GLU70 5.0 10.2 1.0

Magnesium binding site 3 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.5
occ:1.00
 F A:F407 2.0 12.5 1.0
OE1 A:GLU66 2.1 12.1 1.0
O A:HOH583 2.1 14.2 1.0
O65 A:U6J401 2.1 11.1 1.0
O A:HOH659 2.1 15.1 1.0
O A:HOH580 2.1 13.7 1.0
CD A:GLU66 3.1 12.3 1.0
PB5 A:U6J401 3.2 11.1 1.0
OE2 A:GLU66 3.5 11.2 1.0
MG A:MG403 3.5 11.2 1.0
O55 A:U6J401 3.7 10.9 1.0
O A:HOH504 3.7 11.9 1.0
O75 A:U6J401 3.7 12.5 1.0
OE2 A:GLU69 4.0 15.2 1.0
NH1 A:ARG65 4.0 12.9 1.0
N A:GLY52 4.1 10.8 1.0
O A:HOH594 4.1 17.9 1.0
O A:HOH531 4.1 26.8 1.0
O A:HOH536 4.3 27.0 1.0
O A:HOH505 4.3 28.4 1.0
O A:GLY52 4.3 11.7 1.0
O A:HOH563 4.4 12.3 1.0
O A:HOH668 4.4 36.5 1.0
CG A:GLU66 4.4 10.6 1.0
O45 A:U6J401 4.5 11.0 1.0
O A:HOH648 4.6 35.6 1.0
O A:HOH699 4.7 25.4 1.0
O A:HOH581 4.7 12.6 1.0
CA A:GLY51 4.7 9.8 1.0
CA A:GLY52 4.8 11.4 1.0
C A:GLY51 4.8 10.0 1.0
NH2 A:ARG65 4.9 13.0 1.0
CZ A:ARG65 4.9 12.4 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 10:25:14 2023

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