Manganese in the structure of Ddctp:O6MEG Pair in the Polymerase Active Site (0 Position) (pdb 2hvh)

The binding sites of Manganese atom in the structure of Ddctp:O6MEG Pair in the Polymerase Active Site (0 Position) (pdb code 2hvh). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2hvh structure was solved by J.J.WARREN, L.J.FORSBERG, L.S.BEESE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.3-2.5 Space group P212121 a (A) 94.060 b (A) 109.390 c (A) 151.310 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 26.2 Manganese Binding Sites: Manganese binding site 1 out of 2 in 2hvh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2hvh. 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: Asp653, A: Tyr654, A: Ser655, A: Gln656, A: Ile657, A: Asp830, A: Dct883, A: Hoh155, conact list: Atom Atom Distance (A) Mn O A:Asp653 4.70 Mn CB A:Asp653 4.73 Mn OD2 A:Asp653 3.78 Mn C A:Asp653 4.14 Mn OD1 A:Asp653 2.88 Mn CG A:Asp653 3.54 Mn CA A:Asp653 4.77 Mn O A:Tyr654 1.84 Mn N A:Tyr654 3.50 Mn CB A:Tyr654 3.88 Mn C A:Tyr654 2.96 Mn CA A:Tyr654 3.59 Mn N A:Ser655 4.08 Mn C A:Ser655 4.95 Mn CA A:Ser655 4.44 Mn N A:Gln656 4.50 Mn CG2 A:Ile657 4.97 Mn O A:Asp830 4.00 Mn CB A:Asp830 4.08 Mn OD2 A:Asp830 3.61 Mn C A:Asp830 4.74 Mn OD1 A:Asp830 3.18 Mn CG A:Asp830 3.36 Mn PG A:Dct883 3.81 Mn O3B A:Dct883 2.88 Mn O2G A:Dct883 3.66 Mn PA A:Dct883 4.14 Mn O3G A:Dct883 4.51 Mn O2A A:Dct883 3.20 Mn O1B A:Dct883 4.92 Mn PB A:Dct883 3.48 Mn O2B A:Dct883 3.12 Mn O3A A:Dct883 3.79 Mn O A:Hoh155 4.15 interactive model: Manganese binding site 2 out of 2 in 2hvh Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2hvh. 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: Asp653, D: Tyr654, D: Ser655, D: Gln656, D: Ile657, D: Asp830, D: Dct881, D: Hoh72, D: Hoh77, conact list: Atom Atom Distance (A) Mn CB D:Asp653 4.67 Mn OD2 D:Asp653 3.53 Mn C D:Asp653 4.60 Mn OD1 D:Asp653 2.32 Mn CG D:Asp653 3.28 Mn O D:Tyr654 2.25 Mn N D:Tyr654 4.20 Mn CB D:Tyr654 4.66 Mn C D:Tyr654 3.43 Mn CA D:Tyr654 4.29 Mn N D:Ser655 4.38 Mn C D:Ser655 4.70 Mn CA D:Ser655 4.52 Mn N D:Gln656 4.19 Mn CA D:Gln656 4.95 Mn N D:Ile657 4.67 Mn CG2 D:Ile657 4.64 Mn O D:Asp830 4.93 Mn CB D:Asp830 4.42 Mn OD2 D:Asp830 2.10 Mn OD1 D:Asp830 3.69 Mn CG D:Asp830 3.20 Mn PG D:Dct881 3.40 Mn O3B D:Dct881 3.69 Mn O2G D:Dct881 2.22 Mn PA D:Dct881 3.38 Mn O3G D:Dct881 4.37 Mn O2A D:Dct881 2.21 Mn O1B D:Dct881 4.54 Mn PB D:Dct881 3.20 Mn C5' D:Dct881 4.08 Mn O5' D:Dct881 4.25 Mn O2B D:Dct881 2.04 Mn O3A D:Dct881 3.66 Mn O1G D:Dct881 4.65 Mn O1A D:Dct881 4.52 Mn O D:Hoh72 4.70 Mn O D:Hoh77 3.26 interactive model: