Magnesium in PDB 8cqx: Ribokinase From T.Sp Mutant A92G

The structure of Ribokinase From T.Sp Mutant A92G, PDB code: 8cqx was solved by V.I.Timofeev, M.B.Shevtsov, Y.A.Abramchik, M.A.Kostromina, E.A.Zayats, I.P.Kuranova, R.S.Esipov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.52 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.307, 155.608, 82.915, 90, 96.37, 90
R / Rfree (%)	22.9 / 31.1

The binding sites of Magnesium atom in the Ribokinase From T.Sp Mutant A92G (pdb code 8cqx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ribokinase From T.Sp Mutant A92G, PDB code: 8cqx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ribokinase From T.Sp Mutant A92G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ribokinase From T.Sp Mutant A92G within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.1 occ:1.00 O A:ASP242 2.4 43.9 1.0 O A:ALA278 2.4 32.0 1.0 O A:THR244 2.5 29.6 1.0 O A:GLY283 2.7 52.3 1.0 OG A:SER287 2.8 35.8 1.0 O A:ARG281 3.1 59.4 1.0 CB A:SER287 3.4 35.7 1.0 C A:ASP242 3.5 45.7 1.0 C A:ALA278 3.7 30.2 1.0 C A:THR244 3.7 30.6 1.0 CB A:ASP242 3.9 47.2 1.0 C A:GLY283 4.0 45.0 1.0 N A:THR244 4.0 31.7 1.0 CG A:ASP242 4.1 46.4 1.0 CA A:THR244 4.2 30.8 1.0 C A:ARG281 4.3 55.2 1.0 OD2 A:ASP242 4.3 44.6 1.0 CA A:ASP242 4.3 44.9 1.0 C A:THR243 4.4 34.3 1.0 N A:GLY283 4.4 43.6 1.0 CB A:THR244 4.5 30.7 1.0 CA A:THR279 4.5 37.0 1.0 N A:THR279 4.5 33.2 1.0 N A:THR243 4.5 39.7 1.0 C A:PRO282 4.6 47.1 1.0 CA A:ALA278 4.6 27.6 1.0 OD1 A:ASP242 4.6 46.9 1.0 O A:ALA284 4.7 36.8 1.0 CB A:ALA278 4.7 27.1 1.0 CA A:THR243 4.8 35.9 1.0 CA A:GLY283 4.8 45.9 1.0 C A:THR279 4.8 38.3 1.0 N A:ALA245 4.8 27.6 1.0 O A:THR243 4.8 34.0 1.0 CA A:SER287 4.9 32.1 1.0 CA A:PRO282 4.9 53.2 1.0 N A:ALA284 4.9 41.7 1.0 O A:PRO282 4.9 44.1 1.0 CB A:ALA245 4.9 29.6 1.0 O A:THR279 5.0 37.2 1.0

Magnesium binding site 2 out of 3 in the Ribokinase From T.Sp Mutant A92G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ribokinase From T.Sp Mutant A92G within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:9.9 occ:1.00 O B:ASP242 2.4 22.8 1.0 O B:THR244 2.5 21.2 1.0 O B:ALA278 2.6 23.7 1.0 O B:GLY283 2.8 29.1 1.0 O B:ARG281 2.8 31.4 1.0 OG B:SER287 2.9 20.5 1.0 CB B:SER287 3.1 22.3 1.0 C B:ASP242 3.5 23.0 1.0 C B:THR244 3.7 21.5 1.0 C B:ALA278 3.8 24.9 1.0 CB B:ASP242 4.0 24.7 1.0 C B:GLY283 4.0 31.7 1.0 N B:THR244 4.0 22.5 1.0 C B:ARG281 4.0 30.1 1.0 CG B:ASP242 4.2 24.4 1.0 N B:GLY283 4.2 29.6 1.0 CA B:THR244 4.2 22.0 1.0 CA B:ASP242 4.3 26.6 1.0 CB B:THR244 4.3 22.4 1.0 C B:THR243 4.3 25.3 1.0 C B:PRO282 4.4 29.1 1.0 N B:THR243 4.4 23.8 1.0 OD1 B:ASP242 4.4 24.2 1.0 CA B:THR279 4.5 22.5 1.0 N B:THR279 4.5 22.6 1.0 OD2 B:ASP242 4.6 24.3 1.0 CA B:SER287 4.6 22.9 1.0 CA B:THR243 4.7 23.9 1.0 C B:THR279 4.7 24.1 1.0 CA B:GLY283 4.7 31.2 1.0 O B:THR279 4.7 22.0 1.0 CA B:ALA278 4.7 22.5 1.0 O B:PRO282 4.8 25.8 1.0 N B:ARG281 4.8 28.8 1.0 CA B:PRO282 4.8 30.8 1.0 N B:ALA245 4.8 20.9 1.0 O B:THR243 4.9 24.2 1.0 N B:PRO282 4.9 31.1 1.0 O B:ALA284 4.9 25.6 1.0 N B:ASP242 4.9 25.5 1.0 CB B:ALA245 4.9 22.3 1.0 CB B:ALA278 5.0 22.2 1.0 CA B:ARG281 5.0 31.3 1.0

Magnesium binding site 3 out of 3 in the Ribokinase From T.Sp Mutant A92G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ribokinase From T.Sp Mutant A92G within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:20.5 occ:1.00 O C:ALA278 2.6 28.3 1.0 O C:ARG281 2.7 26.4 1.0 O C:GLY283 2.7 29.1 1.0 O C:ASP242 2.7 31.2 1.0 O C:THR244 2.7 26.1 1.0 OG C:SER287 2.9 23.8 1.0 CB C:SER287 3.0 24.8 1.0 C C:ASP242 3.8 33.3 1.0 C C:THR244 3.8 27.2 1.0 C C:ALA278 3.9 27.3 1.0 C C:ARG281 3.9 34.3 1.0 C C:GLY283 3.9 30.6 1.0 CB C:ASP242 4.1 32.3 1.0 N C:THR244 4.1 25.9 1.0 CG C:ASP242 4.1 31.2 1.0 N C:GLY283 4.3 32.8 1.0 OD2 C:ASP242 4.3 31.7 1.0 C C:PRO282 4.3 33.9 1.0 CA C:THR244 4.3 30.3 1.0 CB C:THR244 4.5 32.3 1.0 CA C:SER287 4.5 25.0 1.0 OD1 C:ASP242 4.5 28.7 1.0 CA C:ASP242 4.5 33.6 1.0 C C:THR243 4.6 30.0 1.0 O C:PRO282 4.6 35.7 1.0 CA C:THR279 4.6 26.7 1.0 CA C:PRO282 4.7 34.5 1.0 N C:THR243 4.7 30.6 1.0 N C:THR279 4.7 25.6 1.0 N C:ARG281 4.7 30.0 1.0 CA C:GLY283 4.7 31.4 1.0 N C:PRO282 4.7 36.5 1.0 O C:ALA284 4.8 28.9 1.0 CA C:ALA278 4.8 26.1 1.0 CA C:ARG281 4.8 32.8 1.0 C C:THR279 4.9 27.1 1.0 N C:ALA284 4.9 30.7 1.0 CA C:THR243 4.9 31.8 1.0

V.I.Timofeev, M.B.Shevtsov, Y.A.Abramchik, M.A.Kostromina, E.A.Zayats, I.P.Kuranova, R.S.Esipov. Ribokinase From T.Sp Mutant A92G To Be Published.