Magnesium in PDB 2f17: Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom

All present enzymatic activity of Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom:
2.7.6.2;

The structure of Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom, PDB code: 2f17 was solved by J.Y.Liu, D.E.Timm, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.363, 89.363, 141.430, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 25.2

The binding sites of Magnesium atom in the Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom (pdb code 2f17). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom, PDB code: 2f17:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:27.5 occ:0.50 OD1 A:ASP71 2.4 67.0 1.0 OD1 A:ASP73 2.4 68.7 1.0 O3P A:AMP301 2.4 76.9 1.0 OD2 A:ASP46 2.4 48.6 1.0 OD2 A:ASP100 2.4 44.3 1.0 O2A A:PYI902 2.4 64.9 1.0 CG A:ASP73 3.2 68.9 1.0 CG A:ASP71 3.2 66.9 1.0 OD2 A:ASP71 3.3 67.2 1.0 CG A:ASP46 3.5 48.3 1.0 PA A:PYI902 3.6 65.4 1.0 CG A:ASP100 3.6 44.9 1.0 OD2 A:ASP73 3.7 70.8 1.0 P A:AMP301 3.8 76.9 1.0 O3A A:PYI902 3.8 66.6 1.0 CB A:ASP46 3.9 47.2 1.0 O2P A:AMP301 4.2 76.9 1.0 O1A A:PYI902 4.2 66.2 1.0 CB A:ASP73 4.2 67.3 1.0 OD1 A:ASP100 4.3 46.6 1.0 O A:HOH925 4.3 44.8 1.0 O1P A:AMP301 4.4 77.7 1.0 N A:ASP73 4.4 66.0 1.0 CB A:ASP71 4.5 65.8 1.0 C A:ASP73 4.5 65.0 1.0 CB A:SER74 4.6 62.1 1.0 N A:ASP71 4.6 63.4 1.0 OD1 A:ASP46 4.6 49.6 1.0 O2B A:PYI902 4.6 66.9 1.0 CA A:ASP73 4.6 65.9 1.0 O A:ASP73 4.7 65.2 1.0 OG A:SER74 4.7 62.4 1.0 CB A:ASP100 4.7 43.9 1.0 N A:SER74 4.9 63.5 1.0 PB A:PYI902 4.9 66.2 1.0 OM7 A:PYI902 4.9 61.9 1.0 O5' A:AMP301 4.9 76.8 1.0 CA A:ASP71 5.0 65.0 1.0

Magnesium binding site 2 out of 2 in the Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Thiamin Pyrophosphokinase in A Ternary Complex with Pyrithiamin Pyrophosphate and Amp at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:54.2 occ:1.00 OD2 B:ASP46 2.4 54.6 1.0 OD2 B:ASP100 2.4 49.1 1.0 OD2 B:ASP71 2.4 70.6 1.0 O2S B:EPE2201 2.4 0.2 1.0 O2A B:PYI2202 2.4 68.1 1.0 O2B B:PYI2202 2.4 72.5 1.0 CG B:ASP71 3.2 69.0 1.0 S B:EPE2201 3.4 0.4 1.0 CG B:ASP46 3.5 53.1 1.0 O1S B:EPE2201 3.6 0.6 1.0 CG B:ASP100 3.6 47.8 1.0 OD1 B:ASP71 3.6 69.8 1.0 PA B:PYI2202 3.6 68.3 1.0 O1A B:PYI2202 3.8 68.9 1.0 O3S B:EPE2201 3.8 0.1 1.0 PB B:PYI2202 3.8 72.4 1.0 CB B:ASP46 4.1 51.9 1.0 OG B:SER74 4.2 67.3 1.0 OD1 B:ASP100 4.2 49.2 1.0 O3A B:PYI2202 4.4 70.0 1.0 O3B B:PYI2202 4.4 73.0 1.0 CB B:ASP71 4.5 67.3 1.0 CB B:ASP73 4.5 70.2 1.0 N B:ASP73 4.6 68.2 1.0 OD1 B:ASP46 4.6 54.0 1.0 CB B:ASP100 4.7 44.9 1.0 CB B:SER74 4.8 66.8 1.0 N B:ASP71 4.8 64.8 1.0 C B:ASP71 4.8 66.7 1.0 N B:SER74 4.9 67.0 1.0 CA B:ASP71 4.9 66.3 1.0 C B:ASP73 4.9 67.9 1.0 CA B:ASP73 4.9 68.6 1.0 OM7 B:PYI2202 4.9 65.0 1.0 C10 B:EPE2201 5.0 0.4 1.0 O1B B:PYI2202 5.0 72.8 1.0

J.Y.Liu, D.E.Timm, T.D.Hurley. Pyrithiamine As A Substrate For Thiamine Pyrophosphokinase J.Biol.Chem. V. 281 6601 2006.
ISSN: ISSN 0021-9258
PubMed: 16365036
DOI: 10.1074/JBC.M510951200