Manganese in the structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed With A 16NT Dna Duplex. (pdb 2w42)

The binding sites of Manganese atom in the structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed With A 16NT Dna Duplex. (pdb code 2w42). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2w42 structure was solved by J.S.PARKER, S.M.ROE, D.BARFORD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 98.1-1.9 Space group P1 a (A) 51.838 b (A) 61.384 c (A) 103.540 alpha (°) 75.80 beta (°) 75.86 gamma (°) 79.47 Rfactor (%) 20.5 Rfree (%) 24.3 Manganese Binding Sites: Manganese binding site 1 out of 2 in 2w42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2w42. 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: Gln137, A: Gln159, A: Lys163, A: Arg380, A: Leu427, P: Dt1, P: Dt2, P: Dc3, A: Hoh2242, A: Hoh2243, A: Hoh2244, P: Hoh2002, conact list: Atom Atom Distance (A) Mn NE2 A:Gln137 4.45 Mn OE1 A:Gln137 4.65 Mn NE2 A:Gln159 3.38 Mn OE1 A:Gln159 2.04 Mn CB A:Gln159 4.96 Mn CD A:Gln159 3.01 Mn CG A:Gln159 4.36 Mn CE A:Lys163 4.55 Mn NZ A:Lys163 3.94 Mn CZ A:Arg380 4.65 Mn CG A:Arg380 4.89 Mn NE A:Arg380 4.19 Mn NH2 A:Arg380 4.18 Mn O A:Leu427 2.46 Mn CB A:Leu427 4.76 Mn C A:Leu427 2.67 Mn CA A:Leu427 4.19 Mn OXT A:Leu427 2.24 Mn OP1 P:Dt1 3.55 Mn P P:Dt1 3.28 Mn OP2 P:Dt1 4.29 Mn C5' P:Dt1 4.28 Mn O5' P:Dt1 4.24 Mn OP3 P:Dt1 1.98 Mn O3' P:Dt2 3.87 Mn OP1 P:Dc3 2.09 Mn P P:Dc3 3.52 Mn OP2 P:Dc3 4.21 Mn C5' P:Dc3 4.92 Mn O5' P:Dc3 4.61 Mn O A:Hoh2242 4.54 Mn O A:Hoh2243 4.27 Mn O A:Hoh2244 2.20 Mn O P:Hoh2002 4.58 interactive model: Manganese binding site 2 out of 2 in 2w42 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2w42. 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: Gln137, B: Gln159, B: Lys163, B: Arg380, B: Leu427, R: Dt1, R: Dt2, R: Dc3, B: Hoh2141, B: Hoh2142, B: Hoh2143, R: Hoh2005, conact list: Atom Atom Distance (A) Mn NE2 B:Gln137 4.51 Mn OE1 B:Gln137 4.67 Mn NE2 B:Gln159 3.58 Mn OE1 B:Gln159 2.22 Mn CD B:Gln159 3.21 Mn CG B:Gln159 4.56 Mn CE B:Lys163 4.48 Mn NZ B:Lys163 3.89 Mn CZ B:Arg380 4.65 Mn CG B:Arg380 4.73 Mn NE B:Arg380 4.15 Mn NH2 B:Arg380 4.29 Mn O B:Leu427 2.45 Mn CB B:Leu427 4.68 Mn C B:Leu427 2.58 Mn CA B:Leu427 4.07 Mn OXT B:Leu427 1.93 Mn OP1 R:Dt1 3.56 Mn P R:Dt1 3.36 Mn OP2 R:Dt1 4.33 Mn C5' R:Dt1 4.42 Mn O5' R:Dt1 4.32 Mn OP3 R:Dt1 2.13 Mn O3' R:Dt2 3.98 Mn OP1 R:Dc3 2.13 Mn P R:Dc3 3.41 Mn OP2 R:Dc3 4.20 Mn C5' R:Dc3 4.80 Mn O5' R:Dc3 4.53 Mn O B:Hoh2141 4.33 Mn O B:Hoh2142 4.50 Mn O B:Hoh2143 2.21 Mn O R:Hoh2005 4.61 interactive model: