Manganese in the structure of T. Maritima Rnase H2 D107N in Complex With Nucleic Acid Substrate and Manganese Ions (pdb 3o3h)

The binding sites of Manganese atom in the structure of T. Maritima Rnase H2 D107N in Complex With Nucleic Acid Substrate and Manganese Ions (pdb code 3o3h). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3o3h structure was solved by M.P.RYCHLIK, H.CHON, S.M.CERRITELLI, P.KLIMEK, R.J.CROUCH, M.NOWOTNY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.2-2.8 Space group C121 a (A) 104.658 b (A) 48.571 c (A) 77.910 alpha (°) 90.00 beta (°) 131.97 gamma (°) 90.00 Rfactor (%) 18.2 Rfree (%) 25.3 Manganese Binding Sites: Manganese binding site 1 out of 3 in 3o3h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3o3h. 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: Asp45, A: Lys47, A: Asn107, A: Lys122, A: Asp124, A: Gln125, D: Dc5, D: C6, A: Mn224, A: Hoh246, A: Hoh257, conact list: Atom Atom Distance (A) Mn OD1 A:Asp45 4.26 Mn CG A:Asp45 4.77 Mn CE A:Lys47 4.82 Mn NZ A:Lys47 4.03 Mn ND2 A:Asn107 4.69 Mn OD1 A:Asn107 4.70 Mn C A:Lys122 4.94 Mn CA A:Lys122 4.37 Mn CB A:Asp124 4.43 Mn OD2 A:Asp124 2.40 Mn OD1 A:Asp124 2.74 Mn CG A:Asp124 2.92 Mn NE2 A:Gln125 4.18 Mn OP1 D:Dc5 4.82 Mn OP2 D:Dc5 4.96 Mn OP1 D:C6 4.31 Mn P D:C6 4.35 Mn OP2 D:C6 3.37 Mn MN A:Mn224 4.68 Mn O A:Hoh246 2.55 Mn O A:Hoh257 3.72 interactive model: Manganese binding site 2 out of 3 in 3o3h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3o3h. 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: Asp18, A: Glu19, A: Asp45, A: Ser46, A: Lys47, A: Asn107, A: Asp124, A: Ser134, D: Dc5, D: C6, D: Dt7, A: Mn1, A: Hoh253, conact list: Atom Atom Distance (A) Mn CB A:Asp18 4.86 Mn OD2 A:Asp18 3.35 Mn OD1 A:Asp18 2.84 Mn CG A:Asp18 3.45 Mn O A:Glu19 4.58 Mn OD1 A:Asp45 3.36 Mn CG A:Asp45 4.60 Mn OG A:Ser46 4.73 Mn CE A:Lys47 4.65 Mn NZ A:Lys47 4.50 Mn ND2 A:Asn107 4.03 Mn CG A:Asn107 4.91 Mn CB A:Asp124 3.96 Mn OD2 A:Asp124 3.02 Mn OD1 A:Asp124 4.79 Mn CG A:Asp124 3.76 Mn CB A:Ser134 4.13 Mn OG A:Ser134 3.85 Mn CA A:Ser134 4.94 Mn O3' D:Dc5 4.88 Mn OP1 D:C6 2.39 Mn P D:C6 3.69 Mn OP2 D:C6 4.34 Mn C5' D:C6 4.72 Mn O5' D:C6 4.27 Mn P D:Dt7 4.84 Mn OP2 D:Dt7 3.37 Mn MN A:Mn1 4.68 Mn O A:Hoh253 2.49 interactive model: Manganese binding site 3 out of 3 in 3o3h Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3o3h. 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: Dt9, C: Dg10, A: Hoh232, C: Hoh17, conact list: Atom Atom Distance (A) Mn C3' C:Dt9 4.60 Mn C2' C:Dt9 4.73 Mn P C:Dg10 4.96 Mn OP2 C:Dg10 3.68 Mn O A:Hoh232 4.32 Mn O C:Hoh17 4.10 interactive model: