Magnesium in PDB 5ysp: Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol

The structure of Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol, PDB code: 5ysp was solved by R.Nagata, M.Fujihashi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.673, 63.009, 89.884, 90.00, 105.05, 90.00
R / Rfree (%)	19.6 / 21

The binding sites of Magnesium atom in the Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol (pdb code 5ysp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol, PDB code: 5ysp:

Magnesium binding site 1 out of 1 in the Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrophosphate-Dependent Kinase in the Ribokinase Family Complexed with A Pyrophosphate Analog and Myo-Inositol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:30.2 occ:1.00 O A:HOH429 1.8 30.5 1.0 O2 A:MDN302 2.0 32.6 1.0 O8 A:MDN302 2.0 28.1 1.0 O A:HOH428 2.1 30.7 1.0 O A:HOH443 2.2 28.5 1.0 O A:HOH414 2.4 28.2 1.0 P1 A:MDN302 3.2 33.8 1.0 P5 A:MDN302 3.3 30.8 1.0 O1 A:MDN302 3.6 33.2 1.0 C4 A:MDN302 3.7 31.2 1.0 NZ A:LYS171 3.8 26.1 1.0 O7 A:MDN302 4.0 29.9 1.0 OE2 A:GLU176 4.0 23.2 1.0 OD2 A:ASP139 4.0 26.8 1.0 OD2 A:ASP173 4.1 26.4 1.0 OD1 A:ASP139 4.1 24.2 1.0 OE1 A:GLU176 4.3 23.2 1.0 O A:HOH404 4.5 38.2 1.0 O6 A:MDN302 4.5 30.6 1.0 CG A:ASP139 4.5 23.9 1.0 OE1 A:GLN141 4.5 26.4 1.0 O3 A:MDN302 4.6 31.7 1.0 CD A:GLU176 4.6 23.3 1.0 CG A:ASP173 4.6 25.4 1.0 CB A:ASP173 4.8 25.4 1.0 CE A:LYS171 4.8 25.9 1.0 CA A:GLY233 4.8 25.2 1.0 O1 A:INS301 4.8 29.9 1.0 CB A:GLN141 4.9 23.4 1.0 CD A:GLN141 5.0 26.0 1.0

R.Nagata, M.Fujihashi, T.Sato, H.Atomi, K.Miki. Identification of A Pyrophosphate-Dependent Kinase and Its Donor Selectivity Determinants. Nat Commun V. 9 1765 2018.
ISSN: ESSN 2041-1723
PubMed: 29720581
DOI: 10.1038/S41467-018-04201-Z