Manganese in the structure of Mannosylglycerate Synthase in Complex With Mn-Gdp (pdb 2xw4)

The binding sites of Manganese atom in the structure of Mannosylglycerate Synthase in Complex With Mn-Gdp (pdb code 2xw4). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2xw4 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) 49.7-2.8 Space group P3221 a (A) 149.756 b (A) 149.756 c (A) 154.710 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.21 Rfree (%) 21.38 Manganese Binding Sites: Manganese binding site 1 out of 2 in 2xw4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2xw4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp100, A: Asp102, A: Lys215, A: His217, A: Arg218, A: Gdp401, A: Hoh2066, A: Hoh2067, conact list: Atom Atom Distance (A) Mn OD2 A:Asp100 4.67 Mn CB A:Asp102 4.57 Mn OD2 A:Asp102 2.37 Mn OD1 A:Asp102 3.14 Mn CG A:Asp102 3.11 Mn NZ A:Lys215 3.92 Mn NE2 A:His217 4.60 Mn CB A:His217 3.57 Mn ND1 A:His217 2.50 Mn CD2 A:His217 4.59 Mn CE1 A:His217 3.50 Mn CG A:His217 3.41 Mn CA A:His217 4.89 Mn N A:Arg218 4.38 Mn CZ A:Arg218 4.94 Mn NH1 A:Arg218 4.75 Mn O3B A:Gdp401 4.58 Mn PA A:Gdp401 3.43 Mn O2A A:Gdp401 2.38 Mn O1B A:Gdp401 4.05 Mn PB A:Gdp401 3.38 Mn C5' A:Gdp401 4.45 Mn O5' A:Gdp401 4.39 Mn O2B A:Gdp401 2.30 Mn O3A A:Gdp401 3.51 Mn O1A A:Gdp401 4.52 Mn O A:Hoh2066 2.86 Mn O A:Hoh2067 2.36 interactive model: Manganese binding site 2 out of 2 in 2xw4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2xw4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp100, B: Asp102, B: Lys215, B: His217, B: Arg218, B: Gdp401, conact list: Atom Atom Distance (A) Mn OD2 B:Asp100 4.39 Mn CB B:Asp102 4.42 Mn OD2 B:Asp102 2.77 Mn OD1 B:Asp102 2.87 Mn CG B:Asp102 3.07 Mn CE B:Lys215 4.76 Mn NZ B:Lys215 3.50 Mn NE2 B:His217 4.42 Mn CB B:His217 3.20 Mn ND1 B:His217 4.81 Mn CD2 B:His217 3.12 Mn C B:His217 4.89 Mn CG B:His217 3.46 Mn CA B:His217 4.51 Mn N B:Arg218 4.37 Mn O3B B:Gdp401 4.71 Mn PA B:Gdp401 3.86 Mn O2A B:Gdp401 2.58 Mn O1B B:Gdp401 4.42 Mn PB B:Gdp401 3.68 Mn C5' B:Gdp401 4.63 Mn O5' B:Gdp401 4.69 Mn O2B B:Gdp401 2.30 Mn O3A B:Gdp401 4.17 Mn O1A B:Gdp401 4.99 interactive model: