Magnesium in PDB 7aup: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7

All present enzymatic activity of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7:
3.6.1.52; 3.6.1.60;

The structure of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7, PDB code: 7aup was solved by M.A.Marquez-Monino, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.72 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.702, 61.702, 95.844, 90, 90, 120
R / Rfree (%)	22.3 / 26.8

The binding sites of Magnesium atom in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7 (pdb code 7aup). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7, PDB code: 7aup:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:83.4 occ:1.00 O51 A:VEB201 1.8 71.6 0.4 O21 A:VEB201 1.8 124.8 0.6 OE1 A:GLU84 2.3 40.2 1.0 O A:LYS63 2.5 41.3 1.0 O A:HOH339 2.6 31.7 0.5 O26 A:VEB201 2.6 76.6 0.6 O61 A:VEB201 2.8 86.8 0.6 O26 A:VEB201 2.9 74.5 0.4 PB1 A:VEB201 3.2 68.1 0.4 O31 A:VEB201 3.2 53.0 0.4 CD A:GLU84 3.2 38.8 1.0 PA1 A:VEB201 3.3 122.6 0.6 OE2 A:GLU84 3.5 37.3 1.0 O16 A:VEB201 3.6 70.9 0.4 C A:LYS63 3.6 32.4 1.0 O71 A:VEB201 3.7 65.9 0.4 O16 A:VEB201 3.7 85.1 0.6 PA6 A:VEB201 3.7 74.5 0.6 PA6 A:VEB201 3.9 71.0 0.4 O A:HOH301 4.0 64.8 1.0 CA A:GLY64 4.0 30.5 1.0 NZ A:LYS63 4.0 40.0 1.0 PB1 A:VEB201 4.1 95.1 0.6 CB1 A:VEB201 4.1 65.1 0.4 NH2 A:ARG152 4.1 40.2 1.0 O31 A:VEB201 4.1 116.2 0.6 O11 A:VEB201 4.2 115.3 0.6 CB1 A:VEB201 4.2 105.0 0.6 N A:GLY64 4.3 30.9 1.0 PA1 A:VEB201 4.3 64.0 0.4 O61 A:VEB201 4.3 62.2 0.4 O36 A:VEB201 4.3 62.0 0.6 CG A:LYS63 4.3 39.9 1.0 OE2 A:GLU80 4.5 51.1 1.0 CG A:GLU84 4.6 33.9 1.0 O46 A:VEB201 4.6 70.8 0.4 N A:LYS63 4.7 29.6 1.0 CA A:LYS63 4.7 31.1 1.0 C1 A:VEB201 4.8 102.9 0.6 O71 A:VEB201 4.9 94.3 0.6 MG A:MG203 4.9 48.0 0.6 C6 A:VEB201 4.9 90.3 0.6 C6 A:VEB201 4.9 62.7 0.4

Magnesium binding site 2 out of 2 in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Pcp-INSP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:48.0 occ:0.60 O51 A:VEB201 1.8 81.6 0.6 O A:HOH301 2.1 64.8 1.0 PB1 A:VEB201 2.3 95.1 0.6 O61 A:VEB201 2.3 86.8 0.6 OE1 A:GLU80 2.3 46.3 1.0 O71 A:VEB201 3.0 94.3 0.6 O A:HOH307 3.0 46.0 1.0 CD A:GLU80 3.3 44.5 1.0 OE2 A:GLU80 3.6 51.1 1.0 CB1 A:VEB201 3.9 105.0 0.6 NH1 A:ARG79 4.2 43.8 1.0 CA A:GLY64 4.3 30.5 1.0 N A:GLY65 4.3 30.2 1.0 OE1 A:GLU83 4.3 67.3 1.0 O51 A:VEB201 4.6 71.6 0.4 OE1 A:GLU84 4.6 40.2 1.0 CG A:GLU80 4.6 34.7 1.0 O31 A:VEB201 4.7 53.0 0.4 CB1 A:VEB201 4.7 65.1 0.4 C A:GLY64 4.7 31.3 1.0 O21 A:VEB201 4.7 59.5 0.4 O21 A:VEB201 4.8 124.8 0.6 O A:GLY65 4.9 33.5 1.0 MG A:MG202 4.9 83.4 1.0 PA1 A:VEB201 5.0 64.0 0.4

M.A.Marquez-Monino, R.Ortega-Garcia, M.L.Shipton, E.Franco-Echevarria, A.M.Riley, J.Sanz-Aparicio, B.V.L.Potter, B.Gonzalez. Multiple Substrate Recognition By Yeast Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase Through Phosphate Clamping. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33893105
DOI: 10.1126/SCIADV.ABF6744