Manganese in the structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form At Acidic pH (pdb 1v6j)

The binding sites of Manganese atom in the structure of Peanut Lectin-Lactose Complex Crystallized in Orthorhombic Form At Acidic pH (pdb code 1v6j). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1v6j structure was solved by S.KUNDHAVAI NATCHIAR, A.AROCKIA JEYAPRAKASH, T.N.C.RAMYA, C.J.THOMAS, K.SUGUNA, A.SUROLIA, M.VIJAYAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.9 Space group P21212 a (A) 128.733 b (A) 125.531 c (A) 76.050 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 22 Manganese Binding Sites: Manganese binding site 1 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1v6j. 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: Glu121, A: Asp123, A: Asp132, A: Pro133, A: His137, A: Val145, A: Ser147, A: Ca237, A: Hoh243, conact list: Atom Atom Distance (A) Mn OE1 A:Glu121 3.39 Mn OE2 A:Glu121 2.27 Mn CD A:Glu121 3.16 Mn CG A:Glu121 4.53 Mn CB A:Asp123 3.76 Mn OD2 A:Asp123 2.40 Mn OD1 A:Asp123 4.52 Mn CG A:Asp123 3.42 Mn CB A:Asp132 4.52 Mn OD2 A:Asp132 3.79 Mn OD1 A:Asp132 2.20 Mn CG A:Asp132 3.30 Mn CA A:Asp132 4.74 Mn CD A:Pro133 4.72 Mn NE2 A:His137 2.52 Mn ND1 A:His137 4.63 Mn CD2 A:His137 3.42 Mn CE1 A:His137 3.53 Mn CG A:His137 4.61 Mn O A:Val145 3.89 Mn CB A:Ser147 4.82 Mn OG A:Ser147 3.71 Mn CA A:Ca237 4.79 Mn O A:Hoh243 3.96 interactive model: Manganese binding site 2 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1v6j. 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: Glu121, B: Asp123, B: Asp132, B: Pro133, B: His137, B: Val145, B: Ser147, B: Ca237, B: Hoh241, conact list: Atom Atom Distance (A) Mn OE1 B:Glu121 3.32 Mn OE2 B:Glu121 2.30 Mn CD B:Glu121 3.13 Mn CG B:Glu121 4.50 Mn CB B:Asp123 3.87 Mn OD2 B:Asp123 2.48 Mn OD1 B:Asp123 4.64 Mn CG B:Asp123 3.53 Mn CB B:Asp132 4.61 Mn OD2 B:Asp132 3.80 Mn OD1 B:Asp132 2.26 Mn CG B:Asp132 3.36 Mn CA B:Asp132 4.83 Mn CD B:Pro133 4.90 Mn NE2 B:His137 2.60 Mn ND1 B:His137 4.72 Mn CD2 B:His137 3.49 Mn CE1 B:His137 3.62 Mn CG B:His137 4.69 Mn O B:Val145 3.66 Mn C B:Val145 4.84 Mn CB B:Ser147 4.96 Mn OG B:Ser147 3.75 Mn CA B:Ca237 4.70 Mn O B:Hoh241 3.82 interactive model: Manganese binding site 3 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1v6j. 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: Glu121, C: Asp123, C: Asp132, C: Pro133, C: His137, C: Val145, C: Ser147, C: Ca237, conact list: Atom Atom Distance (A) Mn OE1 C:Glu121 3.30 Mn OE2 C:Glu121 2.19 Mn CD C:Glu121 3.08 Mn CG C:Glu121 4.45 Mn CB C:Asp123 3.86 Mn OD2 C:Asp123 2.52 Mn OD1 C:Asp123 4.66 Mn CG C:Asp123 3.54 Mn CB C:Asp132 4.56 Mn OD2 C:Asp132 3.73 Mn OD1 C:Asp132 2.21 Mn CG C:Asp132 3.30 Mn CA C:Asp132 4.87 Mn CD C:Pro133 4.81 Mn NE2 C:His137 2.64 Mn ND1 C:His137 4.75 Mn CD2 C:His137 3.51 Mn CE1 C:His137 3.66 Mn CG C:His137 4.71 Mn O C:Val145 3.91 Mn CB C:Ser147 4.83 Mn OG C:Ser147 3.69 Mn CA C:Ca237 4.75 interactive model: Manganese binding site 4 out of 4 in 1v6j Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 1v6j. 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: Glu121, D: Asp123, D: Asp132, D: Pro133, D: His137, D: Val145, D: Ser147, D: Thr150, D: Ca237, D: Hoh254, conact list: Atom Atom Distance (A) Mn OE1 D:Glu121 3.37 Mn OE2 D:Glu121 2.24 Mn CD D:Glu121 3.12 Mn CG D:Glu121 4.46 Mn CB D:Asp123 3.93 Mn OD2 D:Asp123 2.76 Mn OD1 D:Asp123 4.89 Mn CG D:Asp123 3.74 Mn CB D:Asp132 4.56 Mn OD2 D:Asp132 3.70 Mn OD1 D:Asp132 2.52 Mn CG D:Asp132 3.36 Mn CA D:Asp132 4.70 Mn CD D:Pro133 4.52 Mn NE2 D:His137 2.52 Mn ND1 D:His137 4.62 Mn CD2 D:His137 3.43 Mn CE1 D:His137 3.52 Mn CG D:His137 4.62 Mn O D:Val145 3.83 Mn CB D:Ser147 4.67 Mn OG D:Ser147 3.65 Mn CG2 D:Thr150 4.92 Mn CA D:Ca237 4.99 Mn O D:Hoh254 3.77 interactive model: