Manganese in the structure of Crystal Structure of Dioclea Violacea Seed Lectin (pdb 2gdf)

The binding sites of Manganese atom in the structure of Crystal Structure of Dioclea Violacea Seed Lectin (pdb code 2gdf). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2gdf structure was solved by F.GALLEGO DEL SOL, J.J.C.CHORNET, B.S.CAVADA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 45.0-2.4 Space group P32 a (A) 72.938 b (A) 72.938 c (A) 161.362 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.7 Rfree (%) 25.8 Manganese Binding Sites: Manganese binding site 1 out of 2 in 2gdf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2gdf. 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: Glu8, B: Asp10, B: Asp19, B: His24, B: Ile32, B: Ser34, B: Ca302, B: Hoh308, conact list: Atom Atom Distance (A) Mn OE1 B:Glu8 3.45 Mn OE2 B:Glu8 2.52 Mn CD B:Glu8 3.33 Mn CG B:Glu8 4.73 Mn CB B:Asp10 3.66 Mn OD2 B:Asp10 1.94 Mn OD1 B:Asp10 4.16 Mn CG B:Asp10 3.09 Mn CB B:Asp19 4.24 Mn OD2 B:Asp19 3.33 Mn OD1 B:Asp19 2.66 Mn CG B:Asp19 3.12 Mn CA B:Asp19 4.62 Mn NE2 B:His24 2.32 Mn ND1 B:His24 4.40 Mn CD2 B:His24 3.29 Mn CE1 B:His24 3.29 Mn CG B:His24 4.44 Mn O B:Ile32 4.53 Mn OG B:Ser34 3.95 Mn CA B:Ca302 4.16 Mn O B:Hoh308 2.28 interactive model: Manganese binding site 2 out of 2 in 2gdf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2gdf. 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: D: Glu8, D: Asp10, D: Asp19, D: His24, D: Ile32, D: Ser34, D: Ca1302, D: Hoh1304, conact list: Atom Atom Distance (A) Mn OE1 D:Glu8 3.60 Mn OE2 D:Glu8 2.51 Mn CD D:Glu8 3.39 Mn CG D:Glu8 4.74 Mn CB D:Asp10 3.60 Mn OD2 D:Asp10 1.85 Mn OD1 D:Asp10 4.07 Mn CG D:Asp10 3.01 Mn CB D:Asp19 4.30 Mn OD2 D:Asp19 3.36 Mn OD1 D:Asp19 2.76 Mn CG D:Asp19 3.20 Mn CA D:Asp19 4.67 Mn NE2 D:His24 2.30 Mn ND1 D:His24 4.41 Mn CD2 D:His24 3.24 Mn CE1 D:His24 3.30 Mn CG D:His24 4.41 Mn O D:Ile32 4.54 Mn OG D:Ser34 4.11 Mn CA D:Ca1302 4.18 Mn O D:Hoh1304 2.21 interactive model: