Magnesium in PDB 7e4l: Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation

The structure of Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation, PDB code: 7e4l was solved by R.Tashiro, K.Miki, M.Fujihashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.65 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.205, 46.398, 66.544, 83.53, 80.43, 68.57
R / Rfree (%)	19.2 / 21.6

The binding sites of Magnesium atom in the Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation (pdb code 7e4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation, PDB code: 7e4l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:11.6 occ:1.00 O A:HOH404 2.1 13.3 1.0 O A:HOH480 2.1 13.1 1.0 O2 A:MDN301 2.1 12.0 1.0 O8 A:MDN301 2.1 10.4 1.0 O A:HOH444 2.2 8.4 1.0 O A:HOH437 2.3 9.7 1.0 P1 A:MDN301 3.3 11.7 1.0 P5 A:MDN301 3.4 11.1 1.0 O A:HOH403 3.5 26.0 1.0 NZ A:LYS171 3.6 10.3 1.0 C4 A:MDN301 3.8 11.5 1.0 O3 A:MDN301 3.8 12.4 1.0 OD2 A:ASP139 4.0 11.7 1.0 OE2 A:GLU176 4.0 14.7 1.0 OD1 A:ASP139 4.1 12.9 1.0 O A:HOH431 4.1 24.2 1.0 O7 A:MDN301 4.1 11.3 1.0 OD2 A:ASP173 4.3 14.9 1.0 OE1 A:GLU176 4.3 13.4 1.0 O A:HOH490 4.4 27.2 1.0 CG A:ASP139 4.5 10.8 1.0 O6 A:MDN301 4.5 11.5 1.0 CE A:LYS171 4.6 10.8 1.0 OD1 A:ASP234 4.6 11.1 1.0 O1 A:MDN301 4.6 12.4 1.0 CD A:GLU176 4.6 13.0 1.0 OE1 A:GLN141 4.6 19.6 1.0 CG A:ASP173 4.8 13.1 1.0 CA A:GLY233 4.9 8.8 1.0 O A:HOH405 4.9 27.8 1.0 CB A:ASP173 5.0 12.5 1.0 CB A:GLN141 5.0 15.5 1.0 CD A:GLN141 5.0 18.6 1.0

Magnesium binding site 2 out of 2 in the Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Conversion of Pyrophosphate-Dependent Myo-Inositol-1 Kinase Into Myo- Inositol-3 Kinase By N78L/S89L Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:11.3 occ:1.00 O B:HOH413 2.0 16.9 1.0 O B:HOH483 2.0 15.9 1.0 O6 B:MDN301 2.2 11.3 1.0 O1 B:MDN301 2.2 12.3 1.0 O B:HOH465 2.2 9.8 1.0 O B:HOH424 2.3 10.6 1.0 P1 B:MDN301 3.3 12.7 1.0 P5 B:MDN301 3.4 11.3 1.0 NZ B:LYS171 3.6 10.6 1.0 O2 B:MDN301 3.8 12.4 1.0 C4 B:MDN301 3.8 12.4 1.0 OE2 B:GLU176 4.0 12.7 1.0 OD1 B:ASP139 4.1 13.4 1.0 OD2 B:ASP173 4.1 14.7 1.0 O7 B:MDN301 4.1 11.5 1.0 OD2 B:ASP139 4.1 12.6 1.0 O B:HOH457 4.2 21.9 1.0 OE1 B:GLU176 4.3 11.6 1.0 CG B:ASP139 4.5 11.7 1.0 CE B:LYS171 4.6 10.7 1.0 CD B:GLU176 4.6 12.1 1.0 O8 B:MDN301 4.6 11.9 1.0 O3 B:MDN301 4.6 12.8 1.0 OE1 B:GLN141 4.7 20.3 1.0 CG B:ASP173 4.7 13.3 1.0 OD1 B:ASP234 4.7 13.2 1.0 CB B:GLN141 4.8 16.1 1.0 CA B:GLY233 4.9 10.1 1.0 CB B:ASP173 4.9 12.7 1.0 CD B:GLN141 5.0 18.4 1.0

R.Tashiro, T.Sato, H.Atomi, K.Miki, M.Fujihashi. Altering the Phosphorylation Position of Pyrophosphate-Dependent Myo -Inositol-1-Kinase Based on Its Crystal Structure. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 33877806
DOI: 10.1021/ACSCHEMBIO.0C00733