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Magnesium in PDB 7tn4: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion

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

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4 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) 31.40 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.149, 59.743, 62.769, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 7tn4:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion (pdb code 7tn4). 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7tn4

Go back to Magnesium Binding Sites List in 7tn4
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:13.8
occ:1.00
 O53 A:ZM2507 1.9 15.3 1.0
O43 A:ZM2507 2.0 18.4 1.0
O A:HOH618 2.0 11.3 1.0
O42 A:ZM2507 2.1 16.8 1.0
OE1 A:GLU70 2.1 15.1 1.0
O A:GLY50 2.2 9.9 1.0
CD A:GLU70 3.0 16.4 1.0
PA3 A:ZM2507 3.2 18.8 1.0
PA2 A:ZM2507 3.3 20.3 1.0
OE2 A:GLU70 3.3 15.0 1.0
MG A:MG502 3.3 16.6 1.0
C A:GLY50 3.3 11.0 1.0
PB3 A:ZM2507 3.4 29.3 1.0
O22 A:ZM2507 3.6 20.5 1.0
O23 A:ZM2507 3.6 22.3 1.0
O A:HOH672 3.7 13.6 1.0
CA A:GLY51 3.7 13.4 1.0
O13 A:ZM2507 3.8 19.1 1.0
N A:GLY51 4.0 10.8 1.0
NH1 A:ARG20 4.1 12.4 1.0
O73 A:ZM2507 4.1 22.6 1.0
OE2 A:GLU66 4.1 12.5 1.0
O12 A:ZM2507 4.1 26.1 1.0
O A:HOH623 4.3 14.6 1.0
CG A:GLU70 4.4 15.9 1.0
C2 A:ZM2507 4.4 20.6 1.0
N A:GLY50 4.4 10.9 1.0
O33 A:ZM2507 4.5 18.4 1.0
O32 A:ZM2507 4.5 22.7 1.0
CA A:GLY50 4.5 11.2 1.0
C3 A:ZM2507 4.7 20.7 1.0
F A:F506 4.7 19.6 1.0
O63 A:ZM2507 4.7 21.2 1.0
NH2 A:ARG115 4.9 19.9 1.0
CD A:GLU66 5.0 14.0 1.0

Magnesium binding site 2 out of 3 in 7tn4

Go back to Magnesium Binding Sites List in 7tn4
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.6
occ:1.00
 O A:HOH663 1.9 18.5 1.0
F A:F506 2.1 19.6 1.0
O53 A:ZM2507 2.1 15.3 1.0
O A:HOH672 2.1 13.6 1.0
OE2 A:GLU66 2.2 12.5 1.0
OE1 A:GLU70 2.2 15.1 1.0
CD A:GLU70 3.2 16.4 1.0
CD A:GLU66 3.2 14.0 1.0
PB3 A:ZM2507 3.2 29.3 1.0
O A:HOH602 3.3 16.9 1.0
MG A:MG501 3.3 13.8 1.0
CG A:GLU70 3.4 15.9 1.0
OE1 A:GLU66 3.6 13.8 1.0
MG A:MG503 3.6 18.7 1.0
O42 A:ZM2507 3.8 16.8 1.0
O63 A:ZM2507 3.8 21.2 1.0
O73 A:ZM2507 3.8 22.6 1.0
OE2 A:GLU69 4.0 20.9 1.0
O A:GLY50 4.1 9.9 1.0
O A:HOH730 4.1 32.6 1.0
O A:HOH638 4.2 24.0 1.0
O A:HOH629 4.2 19.6 1.0
O A:HOH688 4.3 29.8 1.0
OE2 A:GLU70 4.4 15.0 1.0
CG A:GLU66 4.5 12.9 1.0
CA A:GLY51 4.5 13.4 1.0
O23 A:ZM2507 4.7 22.3 1.0
O43 A:ZM2507 4.8 18.4 1.0
CB A:GLU66 4.8 12.3 1.0
C A:GLY50 4.8 11.0 1.0
O A:HOH618 4.9 11.3 1.0
CB A:GLU70 4.9 14.8 1.0
O A:HOH690 5.0 17.4 1.0

Magnesium binding site 3 out of 3 in 7tn4

Go back to Magnesium Binding Sites List in 7tn4
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:18.7
occ:1.00
 F A:F506 1.8 19.6 1.0
O A:HOH660 2.1 23.4 1.0
O63 A:ZM2507 2.1 21.2 1.0
OE1 A:GLU66 2.1 13.8 1.0
O A:HOH629 2.1 19.6 1.0
O A:HOH690 2.2 17.4 1.0
CD A:GLU66 3.1 14.0 1.0
PB3 A:ZM2507 3.3 29.3 1.0
OE2 A:GLU66 3.5 12.5 1.0
MG A:MG502 3.6 16.6 1.0
O A:HOH602 3.8 16.9 1.0
O53 A:ZM2507 3.9 15.3 1.0
OE2 A:GLU69 4.0 20.9 1.0
NH1 A:ARG65 4.0 17.7 1.0
O A:HOH718 4.1 33.3 1.0
O73 A:ZM2507 4.1 22.6 1.0
N A:GLY52 4.1 13.3 1.0
O A:GLY52 4.2 14.2 1.0
O A:HOH663 4.3 18.5 1.0
CG A:GLU66 4.5 12.9 1.0
O A:HOH730 4.6 32.6 1.0
O23 A:ZM2507 4.7 22.3 1.0
O A:HOH672 4.8 13.6 1.0
CA A:GLY51 4.8 13.4 1.0
CA A:GLY52 4.8 14.0 1.0
C A:GLY51 4.8 13.2 1.0
NH2 A:ARG65 5.0 17.8 1.0
CZ A:ARG65 5.0 18.0 1.0

Reference:

G.Zong, S.B.Shears, H.Wang. Structural and Catalytic Analyses of the Insp 6 Kinase Activities of Higher Plant Itpks. Faseb J. V. 36 22380 2022.
ISSN: ESSN 1530-6860
PubMed: 35635723
DOI: 10.1096/FJ.202200393R
Page generated: Thu Oct 3 09:22:00 2024

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