Magnesium in PDB 3udt: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5.

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

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5., PDB code: 3udt was solved by V.Gosein, T.-F.Leung, O.Krajden, G.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.63 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.362, 59.913, 83.146, 90.02, 97.04, 116.81
R / Rfree (%)	21 / 27.6

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

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp and IP5. (pdb code 3udt). 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 A. Thaliana in Complex with Adp and IP5., PDB code: 3udt:
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 A. Thaliana in Complex with Adp 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 A. Thaliana in Complex with Adp and IP5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg913 b:31.7 occ:1.00 OD2 A:ASP407 2.1 25.4 1.0 O2A A:ADP912 2.6 38.8 1.0 CG A:ASP407 2.8 23.7 1.0 CB A:ASP407 2.8 17.5 1.0 OG A:SER370 3.4 14.9 1.0 O2B A:ADP912 3.4 45.0 1.0 O A:ASP368 3.7 13.2 1.0 PA A:ADP912 4.0 43.5 1.0 OD1 A:ASP407 4.0 23.0 1.0 CB A:SER370 4.3 16.2 1.0 CA A:ASP407 4.3 15.7 1.0 N A:SER370 4.5 12.9 1.0 PB A:ADP912 4.6 41.0 1.0 C A:CYS369 4.6 10.7 1.0 O1A A:ADP912 4.7 23.7 1.0 O A:ASP407 4.7 17.2 1.0 O3A A:ADP912 4.7 33.4 1.0 CA A:CYS369 4.7 12.0 1.0 O A:ILE406 4.7 12.5 1.0 C A:ASP368 4.8 13.0 1.0 CE A:LYS168 4.8 13.7 1.0 N A:ASP407 5.0 18.1 1.0

Magnesium binding site 2 out of 2 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Adp 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 A. Thaliana in Complex with Adp and IP5. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg913 b:40.3 occ:1.00 O1A B:ADP912 2.2 37.2 1.0 OD2 B:ASP407 3.2 27.2 1.0 O1B B:ADP912 3.3 44.0 1.0 OG B:SER370 3.5 14.8 1.0 CB B:ASP407 3.6 21.8 1.0 PA B:ADP912 3.7 53.1 1.0 CG B:ASP407 3.7 26.3 1.0 O3' B:ADP912 3.8 42.2 1.0 OE2 B:GLU166 4.0 24.9 1.0 O3A B:ADP912 4.2 39.6 1.0 CB B:SER370 4.3 14.5 1.0 O5' B:ADP912 4.3 43.1 1.0 PB B:ADP912 4.4 41.2 1.0 CD1 B:ILE406 4.4 19.1 1.0 C3' B:ADP912 4.4 43.6 1.0 OD1 B:ASP407 4.7 21.3 1.0 O B:ASP368 4.8 17.1 1.0 C5' B:ADP912 4.8 34.1 1.0 O2A B:ADP912 4.8 41.6 1.0 CG1 B:ILE406 4.9 17.0 1.0

V.Gosein, T.F.Leung, O.Krajden, G.J.Miller. Inositol Phosphate-Induced Stabilization of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase and Its Role in Substrate Specificity. Protein Sci. V. 21 737 2012.
ISSN: ISSN 0961-8368
PubMed: 22362712
DOI: 10.1002/PRO.2049