Magnesium in PDB 5w2h: Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp

All present enzymatic activity of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp:
2.7.1.151;

The structure of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp, PDB code: 5w2h was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.35 / 1.90
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.015, 78.015, 85.915, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp (pdb code 5w2h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp, PDB code: 5w2h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:18.8 occ:1.00 O3B A:ADP703 2.0 20.5 1.0 O2A A:ADP703 2.0 16.9 1.0 O A:HOH903 2.1 21.2 1.0 O A:HOH854 2.2 18.2 1.0 OD2 A:ASP385 2.2 21.6 1.0 O A:HOH925 2.2 19.0 1.0 PB A:ADP703 3.2 23.8 1.0 CG A:ASP385 3.2 18.5 1.0 PA A:ADP703 3.2 17.1 1.0 O3A A:ADP703 3.5 20.1 1.0 MG A:MG702 3.7 30.2 1.0 O A:HOH919 3.7 27.6 1.0 CB A:ASP385 3.7 15.4 1.0 O A:HOH898 3.8 17.8 1.0 O1B A:ADP703 3.9 28.3 1.0 OD2 A:ASP144 4.0 19.1 1.0 OD1 A:ASP385 4.3 20.1 1.0 O1A A:ADP703 4.3 17.5 1.0 O5' A:ADP703 4.3 18.4 1.0 CD1 A:LEU179 4.4 18.0 1.0 O2B A:ADP703 4.4 26.2 1.0 C5' A:ADP703 4.4 19.1 1.0 O A:HOH819 4.6 45.6 1.0 OG A:SER252 4.6 15.5 1.0 O A:HOH859 4.7 31.2 1.0 O3' A:ADP703 4.9 19.9 1.0 CG A:ASP144 5.0 17.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Core Catalytic Domain of Human Inositol Phosphate Multikinase in Complex with Ins(1,4,5)P3 and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:30.2 occ:1.00 O A:HOH919 1.8 27.6 1.0 O A:HOH849 2.1 23.8 1.0 O A:HOH859 2.3 31.2 1.0 OD2 A:ASP385 2.3 21.6 1.0 O1B A:ADP703 2.5 28.3 1.0 OD1 A:ASP385 2.6 20.1 1.0 CG A:ASP385 2.8 18.5 1.0 O A:HOH803 3.0 35.2 1.0 O3B A:ADP703 3.2 20.5 1.0 PB A:ADP703 3.4 23.8 1.0 O A:HOH877 3.6 42.5 1.0 O A:HOH903 3.6 21.2 1.0 MG A:MG701 3.7 18.8 1.0 OE1 A:GLN78 4.1 35.4 1.0 NE2 A:GLN78 4.2 42.0 1.0 O41 A:I3P704 4.2 22.9 1.0 O42 A:I3P704 4.3 27.8 1.0 CB A:ASP385 4.3 15.4 1.0 CD A:GLN78 4.4 32.6 1.0 O3A A:ADP703 4.4 20.1 1.0 O2B A:ADP703 4.5 26.2 1.0 O A:ALA250 4.6 15.1 1.0 O3 A:I3P704 4.7 28.1 1.0 NZ A:LYS75 4.7 23.2 1.0 P4 A:I3P704 4.7 24.4 1.0 O2A A:ADP703 4.8 16.9 1.0 O4 A:I3P704 4.9 26.4 1.0

H.Wang, S.B.Shears. Structural Features of Human Inositol Phosphate Multikinase Rationalize Its Inositol Phosphate Kinase and Phosphoinositide 3-Kinase Activities. J. Biol. Chem. V. 292 18192 2017.
ISSN: ESSN 1083-351X
PubMed: 28882892
DOI: 10.1074/JBC.M117.801845