Magnesium in PDB 5mw8: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5:
2.7.1.158;

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5, PDB code: 5mw8 was solved by E.Franco-Echevarria, J.Sanz-Aparicio, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.99 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.162, 71.495, 61.197, 90.00, 111.37, 90.00
R / Rfree (%)	24.1 / 27.1

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 (pdb code 5mw8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5, PDB code: 5mw8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:48.5 occ:1.00 OD1 A:ASP437 2.3 41.6 1.0 O1B A:ATP501 2.4 50.5 1.0 O1G A:ATP501 2.5 52.8 1.0 O43 A:5MY502 2.8 40.8 1.0 CG A:ASP437 3.4 42.3 1.0 OD1 A:ASP439 3.4 53.4 1.0 NZ A:LYS441 3.6 40.3 1.0 O A:HOH618 3.6 44.4 1.0 OD2 A:ASP437 3.7 42.0 1.0 PB A:ATP501 3.8 49.9 1.0 PG A:ATP501 3.8 53.3 1.0 OD2 A:ASP439 3.9 51.5 1.0 P3 A:5MY502 4.0 40.6 1.0 CG A:ASP439 4.0 48.7 1.0 OD2 A:ASP400 4.1 39.8 1.0 O3B A:ATP501 4.1 51.7 1.0 NH2 A:ARG33 4.2 62.0 1.0 CG A:LYS19 4.4 54.4 1.0 O23 A:5MY502 4.4 40.6 1.0 O13 A:5MY502 4.5 40.6 1.0 O2B A:ATP501 4.5 49.4 1.0 CB A:LYS19 4.6 54.1 1.0 CB A:ASP437 4.7 42.3 1.0 O3G A:ATP501 4.7 51.7 1.0 O3A A:ATP501 4.8 50.0 1.0 CE A:LYS441 4.9 39.1 1.0 O2G A:ATP501 4.9 52.3 1.0

Magnesium binding site 2 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:28.6 occ:1.00 O2A A:ATP501 1.9 51.3 1.0 O3G A:ATP501 2.1 51.7 1.0 OD2 A:ASP437 2.2 42.0 1.0 O A:HOH606 2.5 41.6 1.0 O3B A:ATP501 2.9 51.7 1.0 PG A:ATP501 3.1 53.3 1.0 CG A:ASP437 3.4 42.3 1.0 PA A:ATP501 3.4 51.0 1.0 O3' A:ATP501 3.8 51.1 1.0 CB A:ASP437 3.9 42.3 1.0 OG A:SER402 3.9 37.1 1.0 O1G A:ATP501 4.0 52.8 1.0 O1A A:ATP501 4.0 51.8 1.0 PB A:ATP501 4.0 49.9 1.0 O3A A:ATP501 4.1 50.0 1.0 O2G A:ATP501 4.3 52.3 1.0 CE A:LYS138 4.4 33.1 1.0 C3' A:ATP501 4.4 51.3 1.0 OD1 A:ASP437 4.4 41.6 1.0 O5' A:ATP501 4.4 52.0 1.0 O A:HOH611 4.6 29.3 1.0 O1B A:ATP501 4.6 50.5 1.0 C5' A:ATP501 4.6 51.0 1.0 CB A:SER402 4.8 37.6 1.0 O A:ASP400 4.9 34.4 1.0 OE1 A:GLU136 5.0 47.0 1.0

E.Franco-Echevarria, J.Sanz-Aparicio, C.A.Brearley, J.M.Gonzalez-Rubio, B.Gonzalez. The Crystal Structure of Mammalian Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Reveals A New Zinc-Binding Site and Key Features For Protein Function. J. Biol. Chem. V. 292 10534 2017.
ISSN: ESSN 1083-351X
PubMed: 28450399
DOI: 10.1074/JBC.M117.780395