Magnesium in the structure of Mannosylglycerate Synthase in Complex With Mg-Gdp (pdb 2y4k)

The binding sites of Magnesium atom in the structure of Mannosylglycerate Synthase in Complex With Mg-Gdp (pdb code 2y4k). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2y4k structure was solved by M.M.NIELSEN, M.D.L.SUITS, M.YANG, C.S.BARRY, C.MARTINEZ-FLEITES, L.E.TAILFORD, J.E.FLINT, B.G.DAVIS, G.J.DAVIES, H.J.GILBERT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.8-2.5 Space group P3221 a (A) 149.646 b (A) 149.646 c (A) 154.112 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.087 Rfree (%) 22.479 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2y4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2y4k. 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: Asp100, A: Asp102, A: Lys215, A: Ala216, A: His217, A: Gdp401, A: Hoh2070, conact list: Atom Atom Distance (A) Mg OD2 A:Asp100 4.61 Mg CB A:Asp102 4.64 Mg OD2 A:Asp102 2.39 Mg OD1 A:Asp102 3.23 Mg CG A:Asp102 3.18 Mg CE A:Lys215 4.42 Mg O A:Ala216 4.11 Mg CA A:His217 5.00 Mg O3B A:Gdp401 4.54 Mg PA A:Gdp401 3.95 Mg O2A A:Gdp401 2.74 Mg O1B A:Gdp401 3.66 Mg PB A:Gdp401 3.34 Mg C5' A:Gdp401 4.93 Mg O5' A:Gdp401 4.91 Mg O2B A:Gdp401 2.05 Mg O3A A:Gdp401 4.08 Mg O1A A:Gdp401 4.95 Mg O A:Hoh2070 4.68 interactive model: Magnesium binding site 2 out of 2 in 2y4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2y4k. 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: Asp100, B: Asp102, B: Lys215, B: Gdp401, conact list: Atom Atom Distance (A) Mg CB B:Asp100 4.17 Mg OD2 B:Asp100 3.35 Mg CG B:Asp100 4.08 Mg CB B:Asp102 4.70 Mg OD2 B:Asp102 2.83 Mg OD1 B:Asp102 2.79 Mg CG B:Asp102 3.18 Mg CE B:Lys215 3.94 Mg O3B B:Gdp401 4.15 Mg C3' B:Gdp401 4.62 Mg C3' B:Gdp401 4.56 Mg PA B:Gdp401 3.36 Mg PA B:Gdp401 3.50 Mg O2A B:Gdp401 2.09 Mg O2A B:Gdp401 2.73 Mg O1B B:Gdp401 4.73 Mg PB B:Gdp401 3.50 Mg C5' B:Gdp401 4.00 Mg C5' B:Gdp401 4.05 Mg C4' B:Gdp401 4.66 Mg C4' B:Gdp401 4.72 Mg O5' B:Gdp401 4.05 Mg O5' B:Gdp401 4.29 Mg O2B B:Gdp401 2.35 Mg O3A B:Gdp401 3.73 Mg O3A B:Gdp401 4.93 Mg O1A B:Gdp401 4.54 Mg O1A B:Gdp401 3.21 interactive model: