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Magnesium in PDB 6pcl: Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7

Enzymatic activity of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7

All present enzymatic activity of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7:
3.6.1.52;

Protein crystallography data

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7, PDB code: 6pcl was solved by D.E.Dollins, J.Neubauer, J.Dong, J.D.York, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.560, 59.576, 62.358, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.1

Other elements in 6pcl:

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 (pdb code 6pcl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7, PDB code: 6pcl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6pcl

Go back to Magnesium Binding Sites List in 6pcl
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:12.2
occ:1.00
 O44 A:I7P201 2.0 15.0 1.0
O65 A:I7P201 2.0 14.0 1.0
OE2 A:GLU70 2.1 12.5 1.0
O25 A:I7P201 2.1 13.7 1.0
O A:HOH314 2.1 13.4 1.0
O A:GLY50 2.2 11.6 1.0
MG A:MG203 3.0 10.3 0.1
CD A:GLU70 3.0 11.4 1.0
PA5 A:I7P201 3.2 13.8 1.0
PA4 A:I7P201 3.3 15.4 1.0
PB5 A:I7P201 3.3 15.4 1.0
C A:GLY50 3.4 10.2 1.0
OE1 A:GLU70 3.4 11.7 1.0
O45 A:I7P201 3.5 14.7 1.0
O14 A:I7P201 3.6 15.5 1.0
CA A:GLY51 3.7 11.4 1.0
O34 A:I7P201 3.7 16.6 1.0
O15 A:I7P201 3.9 16.5 1.0
N A:GLY51 4.0 9.9 1.0
O A:HOH346 4.1 32.6 1.0
OE1 A:GLU66 4.1 16.0 1.0
O75 A:I7P201 4.1 18.2 1.0
NH1 A:ARG20 4.2 10.8 1.0
O A:HOH330 4.3 18.0 1.0
CG A:GLU70 4.4 12.4 1.0
O55 A:I7P201 4.4 15.6 1.0
NH2 A:ARG115 4.4 15.8 1.0
N A:GLY50 4.5 10.1 1.0
O35 A:I7P201 4.5 13.3 1.0
O24 A:I7P201 4.5 16.9 1.0
CA A:GLY50 4.5 10.4 1.0
O A:HOH355 4.5 18.6 1.0
C5 A:I7P201 4.7 18.6 1.0
C4 A:I7P201 4.7 17.6 1.0

Magnesium binding site 2 out of 3 in 6pcl

Go back to Magnesium Binding Sites List in 6pcl
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:10.3
occ:0.11
 O A:HOH355 1.8 18.6 1.0
O65 A:I7P201 2.0 14.0 1.0
OE2 A:GLU70 2.0 12.5 1.0
OE1 A:GLU66 2.0 16.0 1.0
CD A:GLU70 3.0 11.4 1.0
MG A:MG202 3.0 12.2 1.0
PB5 A:I7P201 3.1 15.4 1.0
CD A:GLU66 3.1 14.2 1.0
CG A:GLU70 3.3 12.4 1.0
O55 A:I7P201 3.6 15.6 1.0
OE2 A:GLU66 3.6 16.2 1.0
O A:GLY50 3.6 11.6 1.0
MG A:MG204 3.7 14.3 0.1
O75 A:I7P201 3.8 18.2 1.0
O A:HOH358 3.8 20.8 1.0
O A:HOH346 3.9 32.6 1.0
O44 A:I7P201 3.9 15.0 1.0
O A:HOH386 3.9 35.3 1.0
OE1 A:GLU69 4.1 25.7 1.0
OE1 A:GLU70 4.1 11.7 1.0
CA A:GLY51 4.2 11.4 1.0
C A:GLY50 4.3 10.2 1.0
CG A:GLU66 4.4 13.0 1.0
O45 A:I7P201 4.4 14.7 1.0
N A:GLY51 4.6 9.9 1.0
O25 A:I7P201 4.6 13.7 1.0
CB A:GLU66 4.7 11.4 1.0
O A:HOH314 4.7 13.4 1.0
O A:HOH381 4.7 39.3 1.0
CB A:GLU70 4.8 11.3 1.0
NH2 A:ARG115 4.8 15.8 1.0
O A:HOH332 4.8 40.8 1.0
O A:GLU66 4.9 12.1 1.0
CA A:GLU66 5.0 11.5 1.0
OD2 A:ASP109 5.0 17.6 1.0

Magnesium binding site 3 out of 3 in 6pcl

Go back to Magnesium Binding Sites List in 6pcl
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:14.3
occ:0.14
 O A:HOH358 1.9 20.8 1.0
O55 A:I7P201 1.9 15.6 1.0
O A:HOH350 1.9 18.1 1.0
OE2 A:GLU66 2.0 16.2 1.0
CD A:GLU66 3.1 14.2 1.0
PB5 A:I7P201 3.1 15.4 1.0
OE1 A:GLU66 3.4 16.0 1.0
N A:GLY52 3.7 11.7 1.0
O65 A:I7P201 3.7 14.0 1.0
MG A:MG203 3.7 10.3 0.1
NH1 A:ARG65 3.7 16.5 1.0
O A:HOH332 3.8 40.8 1.0
O A:HOH303 3.8 33.5 1.0
O75 A:I7P201 3.8 18.2 1.0
O A:GLY52 3.9 14.3 1.0
O A:HOH355 3.9 18.6 1.0
O A:HOH363 3.9 21.3 1.0
OE1 A:GLU69 4.2 25.7 1.0
C A:GLY51 4.3 10.6 1.0
O45 A:I7P201 4.4 14.7 1.0
CA A:GLY51 4.4 11.4 1.0
CG A:GLU66 4.4 13.0 1.0
CA A:GLY52 4.4 12.0 1.0
NH2 A:ARG65 4.5 15.3 1.0
O A:HOH387 4.6 43.2 1.0
CZ A:ARG65 4.6 15.5 1.0
C A:GLY52 4.6 12.6 1.0

Reference:

D.E.Dollins, W.Bai, P.C.Fridy, J.C.Otto, J.L.Neubauer, S.G.Gattis, K.P.M.Mehta, J.D.York. VIP1 Is A Kinase and Pyrophosphatase Switch That Regulates Inositol Diphosphate Signaling. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32303658
DOI: 10.1073/PNAS.1908875117
Page generated: Tue Oct 1 14:03:27 2024

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