Magnesium in PDB 5mwl: 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: 5mwl 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)	70.38 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.623, 140.758, 68.662, 90.00, 106.53, 90.00
R / Rfree (%)	22.5 / 24.5

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)

4 atoms

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 5mwl). 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: 5mwl:
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:Mg505 b:77.5 occ:0.80 O43 A:5MY502 2.4 0.0 1.0 O1B A:ATP501 2.7 0.2 1.0 O1G A:ATP501 3.1 0.7 1.0 OD2 A:ASP439 3.1 0.2 1.0 OD1 A:ASP439 3.3 0.6 1.0 CG A:ASP439 3.6 0.6 1.0 P3 A:5MY502 3.6 0.1 1.0 CD A:LYS19 3.7 0.9 1.0 OD1 A:ASP437 3.7 0.4 1.0 CB A:LYS19 3.8 0.1 1.0 O23 A:5MY502 3.9 0.6 1.0 PB A:ATP501 3.9 0.2 1.0 NZ A:LYS441 3.9 1.0 1.0 O2B A:ATP501 4.2 0.1 1.0 PG A:ATP501 4.2 0.1 1.0 CG A:LYS19 4.3 0.3 1.0 O3B A:ATP501 4.3 0.4 1.0 O33 A:5MY502 4.6 1.0 1.0 O13 A:5MY502 4.7 0.5 1.0 NH2 A:ARG33 4.8 97.3 1.0 O2G A:ATP501 4.8 0.0 1.0 CG A:ASP437 4.8 0.1 1.0 CE A:LYS19 4.9 0.0 1.0 CE A:LYS441 4.9 0.8 1.0 NZ A:LYS19 5.0 0.9 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:Mg506 b:0.4 occ:1.00 OD2 A:ASP437 2.4 0.7 1.0 OG A:SER402 2.6 65.9 1.0 O2A A:ATP501 2.7 0.1 1.0 O3' A:ATP501 3.0 0.3 1.0 CG A:ASP437 3.4 0.1 1.0 O3G A:ATP501 3.4 0.0 1.0 C3' A:ATP501 3.6 0.3 1.0 CB A:ASP437 3.7 0.6 1.0 CB A:SER402 3.8 64.0 1.0 OE2 A:GLU136 3.9 87.7 1.0 PA A:ATP501 4.2 0.7 1.0 O3B A:ATP501 4.3 0.4 1.0 PG A:ATP501 4.5 0.1 1.0 OD1 A:ASP437 4.5 0.4 1.0 O1A A:ATP501 4.7 0.1 1.0 C2' A:ATP501 4.7 0.4 1.0 C4' A:ATP501 4.8 0.8 1.0 C5' A:ATP501 4.9 1.0 1.0 O5' A:ATP501 4.9 0.1 1.0 CE A:LYS138 4.9 78.5 1.0 N A:SER402 5.0 65.3 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