Magnesium in the structure of Thiamin Phosphate Synthase (pdb 2tps)

The binding sites of Magnesium atom in the structure of Thiamin Phosphate Synthase (pdb code 2tps). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2tps structure was solved by H.-J.CHIU, J.J.REDDICK, T.P.BEGLEY, S.E.EALICK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.2 Space group P43212 a (A) 76.830 b (A) 76.830 c (A) 140.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 22.2 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2tps Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2tps. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys61, A: Asn92, A: Asp93, A: Ile108, A: Gly109, A: Asp112, A: Pop2003, A: Hoh3020, A: Hoh3051, A: Hoh3098, conact list: Atom Atom Distance (A) Mg NZ A:Lys61 3.89 Mg ND2 A:Asn92 4.01 Mg OD1 A:Asn92 4.21 Mg CG A:Asn92 4.52 Mg CB A:Asp93 4.43 Mg OD2 A:Asp93 3.54 Mg OD1 A:Asp93 2.08 Mg CG A:Asp93 3.16 Mg CA A:Asp93 4.89 Mg C A:Ile108 4.61 Mg CA A:Ile108 4.77 Mg N A:Gly109 3.86 Mg CA A:Gly109 4.39 Mg CB A:Asp112 4.42 Mg OD2 A:Asp112 2.10 Mg OD1 A:Asp112 3.37 Mg CG A:Asp112 3.07 Mg O A:Pop2003 3.50 Mg O5 A:Pop2003 4.35 Mg P2 A:Pop2003 3.37 Mg O2 A:Pop2003 2.09 Mg P1 A:Pop2003 3.16 Mg O1 A:Pop2003 4.49 Mg O3 A:Pop2003 3.64 Mg O4 A:Pop2003 4.25 Mg O6 A:Pop2003 2.07 Mg O A:Hoh3020 2.11 Mg O A:Hoh3051 2.04 Mg O A:Hoh3098 3.99 interactive model: Magnesium binding site 2 out of 2 in 2tps Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2tps. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Lys61, B: Asn92, B: Asp93, B: Ile108, B: Gly109, B: Asp112, B: Pop2004, B: Hoh3022, B: Hoh3057, B: Hoh3081, conact list: Atom Atom Distance (A) Mg NZ B:Lys61 4.25 Mg ND2 B:Asn92 3.90 Mg OD1 B:Asn92 4.10 Mg CG B:Asn92 4.38 Mg CB B:Asp93 4.29 Mg OD2 B:Asp93 3.38 Mg OD1 B:Asp93 1.95 Mg CG B:Asp93 3.02 Mg CA B:Asp93 4.82 Mg C B:Ile108 4.61 Mg CA B:Ile108 4.80 Mg N B:Gly109 3.87 Mg CA B:Gly109 4.39 Mg CB B:Asp112 4.56 Mg OD2 B:Asp112 2.20 Mg OD1 B:Asp112 3.45 Mg CG B:Asp112 3.20 Mg O B:Pop2004 3.44 Mg O5 B:Pop2004 4.28 Mg P2 B:Pop2004 3.32 Mg O2 B:Pop2004 2.09 Mg P1 B:Pop2004 3.17 Mg O1 B:Pop2004 4.52 Mg O3 B:Pop2004 3.64 Mg O4 B:Pop2004 4.31 Mg O6 B:Pop2004 2.03 Mg O B:Hoh3022 2.04 Mg O B:Hoh3057 2.15 Mg O B:Hoh3081 4.15 interactive model: