Magnesium in PDB 7aur: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Amp-Pnp

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

The structure of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Amp-Pnp, PDB code: 7aur 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)	46.87 / 1.65
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.958, 61.958, 95.924, 90, 90, 120
R / Rfree (%)	20.9 / 24.2

The structure of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Amp-Pnp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with Amp-Pnp (pdb code 7aur). 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 Amp-Pnp, PDB code: 7aur:
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 Amp-Pnp


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:71.7 occ:1.00 O A:HOH348 2.2 46.3 1.0 O A:HOH352 2.6 48.4 1.0 O2G A:ANP201 2.8 91.9 1.0 O A:HOH383 3.2 61.7 1.0 CL A:CL206 3.2 41.2 1.0 NH2 A:ARG32 3.9 48.1 1.0 C5' A:ANP201 3.9 51.7 1.0 N3B A:ANP201 4.1 67.8 1.0 PG A:ANP201 4.1 92.6 1.0 CA A:GLY64 4.2 27.1 1.0 C4' A:ANP201 4.3 57.6 1.0 NH1 A:ARG32 4.4 44.0 1.0 N A:GLY65 4.5 29.0 1.0 MG A:MG205 4.6 68.4 1.0 O A:LYS63 4.6 32.0 1.0 CZ A:ARG32 4.6 43.8 1.0 C A:GLY64 4.9 26.4 1.0 O3G A:ANP201 4.9 93.9 1.0 O3A A:ANP201 4.9 45.2 1.0 NZ A:LYS63 5.0 33.9 1.0 OE1 A:GLU84 5.0 35.9 1.0

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


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 Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:68.4 occ:1.00 O A:HOH314 2.4 46.8 1.0 OE1 A:GLU80 2.6 45.1 1.0 O A:HOH352 2.6 48.4 1.0 O A:HOH381 2.7 63.1 1.0 O A:HOH308 2.7 59.5 1.0 CD A:GLU80 3.3 34.5 1.0 OE2 A:GLU80 3.4 40.3 1.0 N A:GLY65 4.2 29.0 1.0 NH1 A:ARG79 4.3 35.2 1.0 CA A:GLY64 4.4 27.1 1.0 MG A:MG204 4.6 71.7 1.0 O A:GLY65 4.7 32.0 1.0 C A:GLY64 4.7 26.4 1.0 OE1 A:GLU83 4.7 48.9 1.0 O A:HOH348 4.8 46.3 1.0 CG A:GLU80 4.8 29.7 1.0 OE2 A:GLU67 4.9 48.1 1.0 OE1 A:GLU84 5.0 35.9 1.0

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