Manganese in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2 (pdb 9ica)

The binding sites of Manganese atom in the structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked in the Presence of Datp(Alpha)S and MNCL2 (pdb code 9ica). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 9ica structure was solved by H.PELLETIER, M.R.SAWAYA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group P21212 a (A) 178.479 b (A) 57.751 c (A) 48.511 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.7 Rfree (%) n/a Manganese Binding Sites: Manganese binding site 1 out of 2 in 9ica Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 9ica. 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: Asp190, A: Asp192, A: Mn340, A: Stp338, A: Hoh502, A: Hoh522, A: Hoh654, conact list: Atom Atom Distance (A) Mn O A:Asp190 3.12 Mn N A:Asp190 4.22 Mn CB A:Asp190 4.91 Mn OD2 A:Asp190 4.85 Mn C A:Asp190 4.14 Mn OD1 A:Asp190 2.76 Mn CG A:Asp190 3.95 Mn CA A:Asp190 4.62 Mn OD2 A:Asp192 3.04 Mn CG A:Asp192 4.35 Mn MN A:Mn340 4.43 Mn O1B A:Stp338 4.93 Mn PG A:Stp338 3.25 Mn PB A:Stp338 3.45 Mn O3B A:Stp338 3.51 Mn O2G A:Stp338 4.69 Mn PA A:Stp338 3.04 Mn S1A A:Stp338 1.87 Mn O5' A:Stp338 3.71 Mn O2B A:Stp338 2.92 Mn O3G A:Stp338 2.98 Mn O1G A:Stp338 2.63 Mn O3A A:Stp338 3.35 Mn O2A A:Stp338 4.31 Mn O A:Hoh502 3.84 Mn O A:Hoh522 4.42 Mn O A:Hoh654 4.26 interactive model: Manganese binding site 2 out of 2 in 9ica Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 9ica. 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: P: Dg7, A: Asp190, A: Met191, A: Asp192, A: Asp256, A: Arg258, A: Mn339, A: Stp338, conact list: Atom Atom Distance (A) Mn C3' P:Dg7 3.59 Mn O3' P:Dg7 2.60 Mn O4' P:Dg7 4.72 Mn C5' P:Dg7 4.26 Mn C2' P:Dg7 4.72 Mn C4' P:Dg7 3.55 Mn O5' P:Dg7 4.45 Mn CB A:Asp190 4.82 Mn OD2 A:Asp190 3.27 Mn OD1 A:Asp190 3.52 Mn CG A:Asp190 3.61 Mn O A:Met191 4.72 Mn CB A:Asp192 4.90 Mn OD2 A:Asp192 3.28 Mn OD1 A:Asp192 3.46 Mn CG A:Asp192 3.62 Mn CB A:Asp256 4.32 Mn OD2 A:Asp256 3.15 Mn OD1 A:Asp256 4.44 Mn CG A:Asp256 3.81 Mn NH1 A:Arg258 4.95 Mn MN A:Mn339 4.43 Mn PA A:Stp338 4.45 Mn S1A A:Stp338 3.54 Mn O5' A:Stp338 4.79 Mn O2A A:Stp338 4.60 interactive model: