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Calcium in PDB 7auq: Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+

Enzymatic activity of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+

All present enzymatic activity of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+:
3.6.1.52; 3.6.1.60;

Protein crystallography data

The structure of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+, PDB code: 7auq 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) 46.84 / 2.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.999, 61.999, 95.405, 90, 90, 120
R / Rfree (%) 20.5 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+ (pdb code 7auq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+, PDB code: 7auq:

Calcium binding site 1 out of 1 in 7auq

Go back to Calcium Binding Sites List in 7auq
Calcium binding site 1 out of 1 in the Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1 in Complex with AP5A and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:115.1
occ:1.00
 OE1 A:GLU84 2.3 56.7 1.0
O2E A:5FA201 2.5 81.4 1.0
O A:LYS63 2.7 57.6 1.0
O1D A:5FA201 2.8 102.2 1.0
O A:HOH317 2.9 55.4 1.0
O3G A:5FA201 3.0 105.4 1.0
PD A:5FA201 3.3 118.8 1.0
CD A:GLU84 3.3 53.8 1.0
O3D A:5FA201 3.4 107.6 1.0
O3B A:5FA201 3.4 85.5 1.0
PE A:5FA201 3.6 112.7 1.0
OE2 A:GLU84 3.7 50.6 1.0
C A:LYS63 3.8 46.6 1.0
PG A:5FA201 3.8 100.8 1.0
CA A:GLY64 4.0 45.2 1.0
O2G A:5FA201 4.3 109.0 1.0
N A:GLY64 4.3 49.5 1.0
NH2 A:ARG152 4.4 60.0 1.0
NZ A:LYS63 4.4 54.8 1.0
O A:HOH301 4.4 49.3 1.0
O1E A:5FA201 4.6 91.5 1.0
O3E A:5FA201 4.6 81.8 1.0
OE2 A:GLU80 4.6 89.8 1.0
CG A:GLU84 4.6 51.1 1.0
PB A:5FA201 4.7 70.2 1.0
O3A A:5FA201 4.7 76.2 1.0
CG A:LYS63 4.8 58.0 1.0
O2D A:5FA201 4.8 108.8 1.0
CD A:GLU80 4.9 73.5 1.0
N A:LYS63 4.9 48.2 1.0
CA A:LYS63 4.9 50.5 1.0

Reference:

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
Page generated: Thu Jul 18 23:08:17 2024

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