Magnesium in PDB 4xf7: Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)

All present enzymatic activity of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol):
2.7.1.64;

The structure of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol), PDB code: 4xf7 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)	36.32 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.134, 81.176, 81.109, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.5

The structure of Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) also contains other interesting chemical elements:

Iodine

(I)

22 atoms

The binding sites of Magnesium atom in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol) (pdb code 4xf7). 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 Substrates (Amppcp and Myo- Inositol), PDB code: 4xf7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


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 Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:28.3 occ:1.00 O2B A:ACP302 1.9 32.7 1.0 OE1 A:GLN136 2.2 26.1 1.0 O A:HOH426 2.2 25.9 1.0 O A:HOH448 2.2 27.8 1.0 O A:HOH435 2.2 23.3 1.0 O A:HOH447 2.2 29.6 1.0 CD A:GLN136 3.2 26.2 1.0 PB A:ACP302 3.3 35.9 1.0 C3B A:ACP302 3.8 38.4 1.0 NE2 A:GLN136 3.9 26.0 1.0 OE2 A:GLU169 4.0 33.1 1.0 OD1 A:ASP219 4.1 25.4 1.0 O3 A:INS301 4.1 33.2 1.0 O1B A:ACP302 4.1 31.4 1.0 O2G A:ACP302 4.1 45.3 1.0 OD1 A:ASP134 4.2 25.9 1.0 CE1 A:HIS164 4.2 24.9 1.0 OD2 A:ASP134 4.3 23.7 1.0 CB A:GLN136 4.3 26.0 1.0 CG A:GLN136 4.3 25.7 1.0 OE1 A:GLU169 4.4 32.3 1.0 O3A A:ACP302 4.4 32.0 1.0 CA A:GLY218 4.6 25.6 1.0 CG A:ASP134 4.6 25.0 1.0 ND1 A:HIS164 4.7 24.9 1.0 CD A:GLU169 4.7 33.6 1.0 PG A:ACP302 4.7 44.8 1.0 NH2 A:ARG85 4.7 44.2 0.8 O4 A:INS301 4.7 31.1 1.0 C A:GLY218 4.9 24.7 1.0 N A:ASP219 5.0 24.3 1.0

Magnesium binding site 2 out of 2 in the Myo-Inositol 3-Kinase Bound with Its Substrates (Amppcp and Myo- Inositol)


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 Substrates (Amppcp and Myo- Inositol) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:29.8 occ:1.00 O1B B:ACP302 2.0 30.1 1.0 O B:HOH424 2.0 28.2 1.0 O B:HOH426 2.0 23.1 1.0 O B:HOH428 2.2 29.9 1.0 OE1 B:GLN136 2.2 25.4 1.0 O B:HOH423 2.4 21.6 1.0 CD B:GLN136 3.3 23.9 1.0 PB B:ACP302 3.3 30.9 1.0 C3B B:ACP302 3.9 35.7 1.0 NE2 B:GLN136 4.0 24.3 1.0 OD1 B:ASP134 4.1 21.7 1.0 OE2 B:GLU169 4.1 32.7 1.0 O2B B:ACP302 4.2 31.5 1.0 OD2 B:ASP134 4.2 20.7 1.0 O1G B:ACP302 4.2 39.0 1.0 CE1 B:HIS164 4.2 20.3 1.0 OD1 B:ASP219 4.3 24.2 1.0 CB B:GLN136 4.3 22.8 1.0 CG B:GLN136 4.4 23.4 1.0 CA B:GLY218 4.4 24.5 1.0 O3 B:INS301 4.4 33.3 1.0 O3A B:ACP302 4.4 29.8 1.0 OE1 B:GLU169 4.5 28.4 1.0 CG B:ASP134 4.5 20.7 1.0 ND1 B:HIS164 4.6 20.1 1.0 PG B:ACP302 4.7 44.6 1.0 NH2 B:ARG85 4.7 61.1 1.0 CD B:GLU169 4.7 29.1 1.0 OD2 B:ASP166 4.9 34.9 1.0 C B:GLY218 4.9 23.2 1.0 O4 B:INS301 4.9 31.6 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