Manganese in the structure of Crystal Structure of Basic Winged Bean Lectin Complexed With N-Acetyl- D-Galactosamine (pdb 2dty)

The binding sites of Manganese atom in the structure of Crystal Structure of Basic Winged Bean Lectin Complexed With N-Acetyl- D-Galactosamine (pdb code 2dty). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2dty structure was solved by K.A.KULKARNI, S.KATIYAR, A.SUROLIA, M.VIJAYAN, K.SUGUNA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.6 Space group P21212 a (A) 157.725 b (A) 91.864 c (A) 73.549 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 23.9 Manganese Binding Sites: Manganese binding site 1 out of 4 in 2dty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2dty. 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: Glu122, A: Asp124, A: Trp130, A: Asp131, A: Pro132, A: His136, A: Val144, A: Ser146, A: Ca1303, A: Hoh1402, A: Hoh1403, A: Hoh1404, conact list: Atom Atom Distance (A) Mn OE1 A:Glu122 3.51 Mn OE2 A:Glu122 2.28 Mn CD A:Glu122 3.23 Mn CG A:Glu122 4.57 Mn CB A:Asp124 3.60 Mn OD2 A:Asp124 2.33 Mn OD1 A:Asp124 4.45 Mn CG A:Asp124 3.31 Mn NE1 A:Trp130 4.92 Mn CB A:Asp131 4.27 Mn OD2 A:Asp131 3.66 Mn OD1 A:Asp131 2.22 Mn CG A:Asp131 3.16 Mn CA A:Asp131 4.85 Mn CD A:Pro132 4.78 Mn NE2 A:His136 2.35 Mn ND1 A:His136 4.40 Mn CD2 A:His136 3.39 Mn CE1 A:His136 3.24 Mn CG A:His136 4.50 Mn O A:Val144 4.48 Mn OG A:Ser146 4.19 Mn CA A:Ca1303 4.43 Mn O A:Hoh1402 2.36 Mn O A:Hoh1403 2.48 Mn O A:Hoh1404 4.37 interactive model: Manganese binding site 2 out of 4 in 2dty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2dty. 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: Phe107, B: Glu122, B: Asp124, B: Trp130, B: Asp131, B: Pro132, B: His136, B: Val144, B: Ser146, B: Ca2303, B: Hoh2402, B: Hoh2403, B: Hoh2404, conact list: Atom Atom Distance (A) Mn CZ B:Phe107 4.96 Mn OE1 B:Glu122 3.59 Mn OE2 B:Glu122 2.21 Mn CD B:Glu122 3.25 Mn CG B:Glu122 4.59 Mn CB B:Asp124 3.68 Mn OD2 B:Asp124 2.48 Mn OD1 B:Asp124 4.59 Mn CG B:Asp124 3.44 Mn CD1 B:Trp130 4.80 Mn NE1 B:Trp130 4.68 Mn CB B:Asp131 4.19 Mn OD2 B:Asp131 3.25 Mn OD1 B:Asp131 2.24 Mn CG B:Asp131 2.97 Mn CA B:Asp131 4.83 Mn CD B:Pro132 4.91 Mn NE2 B:His136 2.47 Mn ND1 B:His136 4.50 Mn CD2 B:His136 3.56 Mn CE1 B:His136 3.31 Mn CG B:His136 4.65 Mn O B:Val144 4.31 Mn OG B:Ser146 4.20 Mn CA B:Ca2303 4.43 Mn O B:Hoh2402 2.51 Mn O B:Hoh2403 2.39 Mn O B:Hoh2404 4.10 interactive model: Manganese binding site 3 out of 4 in 2dty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2dty. 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: C: Glu122, C: Asp124, C: Trp130, C: Asp131, C: Pro132, C: His136, C: Val144, C: Ser146, C: Ca3303, C: Hoh3402, C: Hoh3403, conact list: Atom Atom Distance (A) Mn OE1 C:Glu122 3.65 Mn OE2 C:Glu122 2.35 Mn CD C:Glu122 3.35 Mn CG C:Glu122 4.70 Mn CB C:Asp124 3.63 Mn OD2 C:Asp124 2.38 Mn OD1 C:Asp124 4.36 Mn CG C:Asp124 3.29 Mn CD1 C:Trp130 4.92 Mn NE1 C:Trp130 4.86 Mn CB C:Asp131 4.20 Mn OD2 C:Asp131 3.34 Mn OD1 C:Asp131 2.21 Mn CG C:Asp131 3.00 Mn CA C:Asp131 4.82 Mn CD C:Pro132 4.80 Mn NE2 C:His136 2.40 Mn ND1 C:His136 4.39 Mn CD2 C:His136 3.52 Mn CE1 C:His136 3.18 Mn CG C:His136 4.58 Mn O C:Val144 4.41 Mn OG C:Ser146 4.14 Mn CA C:Ca3303 4.17 Mn O C:Hoh3402 2.41 Mn O C:Hoh3403 4.22 interactive model: Manganese binding site 4 out of 4 in 2dty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2dty. 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: Phe107, D: Glu122, D: Asp124, D: Trp130, D: Asp131, D: Pro132, D: His136, D: Val144, D: Ser146, D: Ca4303, D: Hoh4402, D: Hoh4403, D: Hoh4404, conact list: Atom Atom Distance (A) Mn CZ D:Phe107 4.98 Mn OE1 D:Glu122 3.83 Mn OE2 D:Glu122 2.25 Mn CD D:Glu122 3.38 Mn CG D:Glu122 4.64 Mn CB D:Asp124 3.60 Mn OD2 D:Asp124 2.51 Mn OD1 D:Asp124 4.42 Mn CG D:Asp124 3.35 Mn CD1 D:Trp130 4.95 Mn NE1 D:Trp130 4.79 Mn CB D:Asp131 4.31 Mn OD2 D:Asp131 3.57 Mn OD1 D:Asp131 2.24 Mn CG D:Asp131 3.14 Mn CA D:Asp131 4.84 Mn CD D:Pro132 4.75 Mn NE2 D:His136 2.26 Mn ND1 D:His136 4.19 Mn CD2 D:His136 3.47 Mn CE1 D:His136 2.95 Mn CG D:His136 4.46 Mn O D:Val144 4.49 Mn OG D:Ser146 4.30 Mn CA D:Ca4303 4.33 Mn O D:Hoh4402 2.31 Mn O D:Hoh4403 2.35 Mn O D:Hoh4404 3.97 interactive model: