Magnesium in PDB 4xf6: Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)

All present enzymatic activity of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate):
2.7.1.64;

The structure of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate), PDB code: 4xf6 was solved by R.Nagata, M.Fujihashi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.66 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.364, 81.255, 82.046, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25

The structure of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) also contains other interesting chemical elements:

Iodine

(I)

15 atoms

The binding sites of Magnesium atom in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) (pdb code 4xf6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate), PDB code: 4xf6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:30.6 occ:1.00 O3B A:ADP302 2.0 29.7 1.0 O A:HOH422 2.0 28.3 1.0 O8 A:LIP301 2.0 28.8 0.7 OE1 A:GLN136 2.1 26.7 1.0 O A:HOH417 2.3 28.9 1.0 O A:HOH414 2.4 23.6 1.0 CD A:GLN136 3.1 26.6 1.0 PB A:ADP302 3.2 31.8 1.0 P1 A:LIP301 3.4 31.9 0.7 O1B A:ADP302 3.7 31.0 1.0 NE2 A:GLN136 3.8 25.7 1.0 O9 A:LIP301 3.9 32.4 0.7 O2B A:ADP302 3.9 35.9 1.0 OE2 A:GLU169 3.9 32.9 1.0 O1 A:LIP301 4.0 27.3 0.7 O3 A:INS303 4.1 21.1 0.3 CB A:GLN136 4.2 30.1 1.0 OE1 A:GLU169 4.2 31.0 1.0 NH2 A:ARG85 4.2 38.3 1.0 CG A:GLN136 4.2 28.7 1.0 OD2 A:ASP134 4.2 25.1 1.0 O4 A:INS303 4.3 23.0 0.3 CE1 A:HIS164 4.3 28.3 1.0 OD1 A:ASP134 4.4 26.4 1.0 OD1 A:ASP219 4.4 27.8 1.0 CA A:GLY218 4.5 26.9 1.0 O2 A:LIP301 4.5 26.7 0.7 CD A:GLU169 4.5 32.9 1.0 O3A A:ADP302 4.5 32.5 1.0 O7 A:LIP301 4.6 32.0 0.7 CG A:ASP134 4.7 26.7 1.0 OD2 A:ASP166 4.8 36.4 1.0 ND1 A:HIS164 4.8 27.5 1.0 N A:GLY218 4.9 28.4 1.0

Magnesium binding site 2 out of 2 in the Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Myo-Inositol 3-Kinase Bound with Its Products (Adp and 1D-Myo-Inositol 3-Phosphate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:27.0 occ:1.00 O1B B:ADP302 2.0 29.0 1.0 O7 B:LIP301 2.1 22.8 0.7 OE1 B:GLN136 2.1 25.1 1.0 O B:HOH414 2.2 24.1 1.0 O B:HOH406 2.2 22.0 1.0 O B:HOH410 2.2 23.2 1.0 CD B:GLN136 3.2 25.6 1.0 PB B:ADP302 3.3 32.4 1.0 P1 B:LIP301 3.3 24.4 0.7 O9 B:LIP301 3.6 23.2 0.7 O2B B:ADP302 3.8 33.2 1.0 NE2 B:GLN136 3.9 24.5 1.0 O1 B:LIP301 3.9 23.1 0.7 O3B B:ADP302 3.9 33.1 1.0 O3 B:INS303 4.0 21.4 0.3 OE2 B:GLU169 4.1 30.4 1.0 NH2 B:ARG85 4.2 34.3 1.0 OD1 B:ASP134 4.2 24.7 1.0 CB B:GLN136 4.3 28.4 1.0 CG B:GLN136 4.3 27.1 1.0 OD2 B:ASP166 4.3 40.2 1.0 OD2 B:ASP134 4.3 23.8 1.0 OE1 B:GLU169 4.3 26.7 1.0 O4 B:INS303 4.3 23.3 0.3 CE1 B:HIS164 4.3 24.4 1.0 O2 B:LIP301 4.4 25.1 0.7 OD1 B:ASP219 4.4 24.0 1.0 O3A B:ADP302 4.5 30.1 1.0 CA B:GLY218 4.6 24.1 1.0 O8 B:LIP301 4.6 25.0 0.7 CD B:GLU169 4.6 29.3 1.0 CG B:ASP134 4.6 24.2 1.0 ND1 B:HIS164 4.7 23.6 1.0 N B:GLY218 5.0 26.0 1.0

R.Nagata, M.Fujihashi, T.Sato, H.Atomi, K.Miki. Crystal Structure and Product Analysis of An Archaeal Myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-Oh Phosphorylation Biochemistry V. 54 3494 2015.
ISSN: ISSN 0006-2960
PubMed: 25972008
DOI: 10.1021/ACS.BIOCHEM.5B00296