Manganese in the structure of Concanavalin A Complex With 4'-Nitrophenyl-Alpha-D- Glucopyranoside (pdb 1val)

The binding sites of Manganese atom in the structure of Concanavalin A Complex With 4'-Nitrophenyl-Alpha-D- Glucopyranoside (pdb code 1val). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1val structure was solved by P.N.KANELLOPOULOS, P.A.TUCKER, S.J.HAMODRAKAS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-3.0 Space group P21212 a (A) 134.660 b (A) 155.670 c (A) 71.420 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 27.4 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1val Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1val. 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: Glu8, A: Asp10, A: Asp19, A: His24, A: Ser34, A: Ca239, A: Hoh242, A: Hoh243, A: Hoh244, conact list: Atom Atom Distance (A) Mn OE1 A:Glu8 3.80 Mn OE2 A:Glu8 2.28 Mn CD A:Glu8 3.37 Mn CG A:Glu8 4.63 Mn CB A:Asp10 3.38 Mn OD2 A:Asp10 2.05 Mn OD1 A:Asp10 4.10 Mn CG A:Asp10 3.01 Mn CA A:Asp10 4.87 Mn CB A:Asp19 4.41 Mn OD2 A:Asp19 3.29 Mn OD1 A:Asp19 2.31 Mn CG A:Asp19 3.08 Mn CA A:Asp19 4.84 Mn NE2 A:His24 2.31 Mn ND1 A:His24 4.31 Mn CD2 A:His24 3.34 Mn CE1 A:His24 3.17 Mn CG A:His24 4.41 Mn OG A:Ser34 4.65 Mn CA A:Ca239 3.89 Mn O A:Hoh242 2.36 Mn O A:Hoh243 2.42 Mn O A:Hoh244 3.62 interactive model: Manganese binding site 2 out of 4 in 1val Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1val. 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: Val32, B: Ser34, B: Ca239, B: Hoh241, B: Hoh242, B: Hoh244, conact list: Atom Atom Distance (A) Mn OE1 B:Glu8 3.63 Mn OE2 B:Glu8 2.36 Mn CD B:Glu8 3.35 Mn CG B:Glu8 4.71 Mn CB B:Asp10 3.45 Mn OD2 B:Asp10 1.86 Mn OD1 B:Asp10 4.00 Mn CG B:Asp10 2.93 Mn CA B:Asp10 4.93 Mn CB B:Asp19 4.21 Mn OD2 B:Asp19 3.29 Mn OD1 B:Asp19 2.22 Mn CG B:Asp19 2.98 Mn CA B:Asp19 4.60 Mn NE2 B:His24 2.75 Mn ND1 B:His24 4.54 Mn CD2 B:His24 3.96 Mn CE1 B:His24 3.30 Mn CG B:His24 4.89 Mn O B:Val32 4.94 Mn OG B:Ser34 4.69 Mn CA B:Ca239 3.48 Mn O B:Hoh241 2.40 Mn O B:Hoh242 2.47 Mn O B:Hoh244 4.32 interactive model: Manganese binding site 3 out of 4 in 1val Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1val. 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: Glu8, C: Asp10, C: Asp19, C: Pro20, C: His24, C: Ser34, C: Ca239, C: Hoh241, C: Hoh242, C: Hoh243, conact list: Atom Atom Distance (A) Mn OE1 C:Glu8 3.86 Mn OE2 C:Glu8 2.30 Mn CD C:Glu8 3.39 Mn CG C:Glu8 4.61 Mn CB C:Asp10 3.40 Mn OD2 C:Asp10 2.50 Mn OD1 C:Asp10 4.39 Mn CG C:Asp10 3.27 Mn CA C:Asp10 4.92 Mn CB C:Asp19 4.46 Mn OD2 C:Asp19 3.17 Mn OD1 C:Asp19 2.56 Mn CG C:Asp19 3.13 Mn CA C:Asp19 4.93 Mn CD C:Pro20 4.84 Mn NE2 C:His24 2.13 Mn ND1 C:His24 4.24 Mn CD2 C:His24 3.16 Mn CE1 C:His24 3.09 Mn CG C:His24 4.30 Mn OG C:Ser34 4.23 Mn CA C:Ca239 4.37 Mn O C:Hoh241 2.51 Mn O C:Hoh242 2.10 Mn O C:Hoh243 4.24 interactive model: Manganese binding site 4 out of 4 in 1val Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1val. 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: Pro20, D: His24, D: Val32, D: Ser34, D: Ca239, D: Hoh241, D: Hoh243, D: Hoh244, conact list: Atom Atom Distance (A) Mn OE1 D:Glu8 3.60 Mn OE2 D:Glu8 2.20 Mn CD D:Glu8 3.23 Mn CG D:Glu8 4.53 Mn CB D:Asp10 3.26 Mn OD2 D:Asp10 2.03 Mn OD1 D:Asp10 3.97 Mn CG D:Asp10 2.90 Mn CA D:Asp10 4.77 Mn CB D:Asp19 4.28 Mn OD2 D:Asp19 3.49 Mn OD1 D:Asp19 2.07 Mn CG D:Asp19 3.06 Mn CA D:Asp19 4.60 Mn CD D:Pro20 4.96 Mn NE2 D:His24 2.17 Mn ND1 D:His24 4.29 Mn CD2 D:His24 3.19 Mn CE1 D:His24 3.15 Mn CG D:His24 4.33 Mn O D:Val32 4.77 Mn OG D:Ser34 4.21 Mn CA D:Ca239 4.28 Mn O D:Hoh241 2.30 Mn O D:Hoh243 4.71 Mn O D:Hoh244 2.27 interactive model: