Manganese in the structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside (pdb 3d4k)

The binding sites of Manganese atom in the structure of Concanavalin A Complexed to A Synthetic Analog of the Trimannoside (pdb code 3d4k). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3d4k structure was solved by R.KADIRVELRAJ, B.L.FOLEY, J.D.DYEKJAER, R.J.WOODS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.8 Space group P1211 a (A) 60.015 b (A) 63.547 c (A) 126.215 alpha (°) 90.00 beta (°) 86.91 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 23.8 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3d4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3d4k. 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: Val32, A: Ser34, A: Ca239, A: Hoh250, A: Hoh307, A: Hoh365, A: Hoh753, conact list: Atom Atom Distance (A) Mn OE1 A:Glu8 3.53 Mn OE2 A:Glu8 2.20 Mn CD A:Glu8 3.21 Mn CG A:Glu8 4.55 Mn CB A:Asp10 3.54 Mn OD2 A:Asp10 2.10 Mn OD1 A:Asp10 4.26 Mn CG A:Asp10 3.15 Mn CB A:Asp19 4.31 Mn OD2 A:Asp19 2.48 Mn OD1 A:Asp19 2.95 Mn CG A:Asp19 2.97 Mn CA A:Asp19 4.89 Mn NE2 A:His24 2.42 Mn ND1 A:His24 4.46 Mn CD2 A:His24 3.41 Mn CE1 A:His24 3.33 Mn CG A:His24 4.53 Mn O A:Val32 4.59 Mn OG A:Ser34 4.15 Mn CA A:Ca239 4.21 Mn O A:Hoh250 3.90 Mn O A:Hoh307 2.30 Mn O A:Hoh365 2.18 Mn O A:Hoh753 4.07 interactive model: Manganese binding site 2 out of 4 in 3d4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3d4k. 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: Hoh257, B: Hoh264, B: Hoh306, conact list: Atom Atom Distance (A) Mn OE1 B:Glu8 3.57 Mn OE2 B:Glu8 2.21 Mn CD B:Glu8 3.23 Mn CG B:Glu8 4.57 Mn CB B:Asp10 3.58 Mn OD2 B:Asp10 2.13 Mn OD1 B:Asp10 4.28 Mn CG B:Asp10 3.17 Mn CB B:Asp19 4.36 Mn OD2 B:Asp19 3.61 Mn OD1 B:Asp19 2.33 Mn CG B:Asp19 3.19 Mn CA B:Asp19 4.73 Mn NE2 B:His24 2.40 Mn ND1 B:His24 4.40 Mn CD2 B:His24 3.45 Mn CE1 B:His24 3.24 Mn CG B:His24 4.54 Mn O B:Val32 4.58 Mn OG B:Ser34 4.20 Mn CA B:Ca239 4.21 Mn O B:Hoh257 4.01 Mn O B:Hoh264 2.24 Mn O B:Hoh306 2.29 interactive model: Manganese binding site 3 out of 4 in 3d4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3d4k. 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: His24, C: Val32, C: Ser34, C: Ca239, C: Hoh256, C: Hoh281, C: Hoh386, C: Hoh710, conact list: Atom Atom Distance (A) Mn OE1 C:Glu8 3.61 Mn OE2 C:Glu8 2.25 Mn CD C:Glu8 3.28 Mn CG C:Glu8 4.62 Mn CB C:Asp10 3.59 Mn OD2 C:Asp10 2.07 Mn OD1 C:Asp10 4.24 Mn CG C:Asp10 3.14 Mn CB C:Asp19 4.23 Mn OD2 C:Asp19 3.59 Mn OD1 C:Asp19 2.24 Mn CG C:Asp19 3.11 Mn CA C:Asp19 4.70 Mn NE2 C:His24 2.39 Mn ND1 C:His24 4.40 Mn CD2 C:His24 3.47 Mn CE1 C:His24 3.23 Mn CG C:His24 4.55 Mn O C:Val32 4.57 Mn OG C:Ser34 4.11 Mn CA C:Ca239 4.21 Mn O C:Hoh256 2.27 Mn O C:Hoh281 3.95 Mn O C:Hoh386 2.09 Mn O C:Hoh710 4.34 interactive model: Manganese binding site 4 out of 4 in 3d4k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3d4k. 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: Val32, D: Ser34, D: Ca239, D: Hoh253, D: Hoh270, D: Hoh271, D: Hoh755, conact list: Atom Atom Distance (A) Mn OE1 D:Glu8 3.62 Mn OE2 D:Glu8 2.22 Mn CD D:Glu8 3.26 Mn CG D:Glu8 4.59 Mn CB D:Asp10 3.58 Mn OD2 D:Asp10 2.17 Mn OD1 D:Asp10 4.29 Mn CG D:Asp10 3.19 Mn CB D:Asp19 4.25 Mn OD2 D:Asp19 3.47 Mn OD1 D:Asp19 2.25 Mn CG D:Asp19 3.07 Mn CA D:Asp19 4.66 Mn NE2 D:His24 2.32 Mn ND1 D:His24 4.29 Mn CD2 D:His24 3.45 Mn CE1 D:His24 3.08 Mn CG D:His24 4.49 Mn O D:Val32 4.58 Mn OG D:Ser34 4.09 Mn CA D:Ca239 4.18 Mn O D:Hoh253 4.01 Mn O D:Hoh270 2.33 Mn O D:Hoh271 2.16 Mn O D:Hoh755 4.25 interactive model: