Manganese in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and MGCL2 (15 Millimolar) (pdb 1zql)

The binding sites of Manganese atom in the structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With Seven Base Pairs Of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) and MGCL2 (15 Millimolar) (pdb code 1zql). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1zql 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) 20.0-3.3 Space group P21212 a (A) 178.509 b (A) 57.730 c (A) 48.028 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.9 Rfree (%) n/a Manganese Binding Sites: Manganese binding site 1 out of 3 in 1zql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1zql. 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: Asp192, A: Asp256, A: Hoh639, A: Hoh642, conact list: Atom Atom Distance (A) Mn C3' P:Dg7 2.67 Mn O3' P:Dg7 2.41 Mn O4' P:Dg7 4.58 Mn C5' P:Dg7 3.81 Mn C2' P:Dg7 4.13 Mn C4' P:Dg7 3.29 Mn O5' P:Dg7 3.68 Mn OD2 A:Asp190 2.97 Mn OD1 A:Asp190 4.02 Mn CG A:Asp190 3.87 Mn OD2 A:Asp192 3.52 Mn OD1 A:Asp192 3.75 Mn CG A:Asp192 4.01 Mn OD2 A:Asp256 3.66 Mn CG A:Asp256 4.64 Mn O A:Hoh639 3.42 Mn O A:Hoh642 3.40 interactive model: Manganese binding site 2 out of 3 in 1zql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1zql. 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: Da5, P: Dt6, A: Leu100, A: Thr101, A: Arg102, A: Val103, A: Ser104, A: Gly105, A: Ile106, A: Gly107, A: Hoh588, conact list: Atom Atom Distance (A) Mn O3' P:Da5 4.88 Mn OP1 P:Dt6 2.62 Mn P P:Dt6 3.82 Mn OP2 P:Dt6 4.16 Mn O5' P:Dt6 4.80 Mn O A:Leu100 4.56 Mn O A:Thr101 1.95 Mn CB A:Thr101 4.90 Mn CG2 A:Thr101 4.93 Mn OG1 A:Thr101 4.95 Mn C A:Thr101 3.15 Mn CA A:Thr101 4.17 Mn O A:Arg102 3.90 Mn N A:Arg102 3.97 Mn C A:Arg102 3.54 Mn CA A:Arg102 3.93 Mn O A:Val103 2.91 Mn N A:Val103 3.51 Mn CB A:Val103 4.89 Mn C A:Val103 3.18 Mn CA A:Val103 3.92 Mn N A:Ser104 3.55 Mn C A:Ser104 4.43 Mn CA A:Ser104 3.75 Mn N A:Gly105 4.18 Mn C A:Gly105 5.00 Mn O A:Ile106 2.82 Mn N A:Ile106 4.06 Mn CB A:Ile106 4.16 Mn CG2 A:Ile106 4.77 Mn C A:Ile106 3.75 Mn CA A:Ile106 4.14 Mn N A:Gly107 4.90 Mn O A:Hoh588 3.00 interactive model: Manganese binding site 3 out of 3 in 1zql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 1zql. 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: Lys60, A: Lys61, A: Leu62, A: Pro63, A: Val65, conact list: Atom Atom Distance (A) Mn O A:Lys60 3.12 Mn C A:Lys60 4.31 Mn O A:Lys61 3.59 Mn N A:Lys61 5.00 Mn C A:Lys61 3.95 Mn CA A:Lys61 4.66 Mn O A:Leu62 2.52 Mn N A:Leu62 4.37 Mn C A:Leu62 3.58 Mn CA A:Leu62 4.47 Mn N A:Pro63 4.46 Mn CD A:Pro63 4.98 Mn CA A:Pro63 4.59 Mn O A:Val65 3.87 Mn N A:Val65 4.76 Mn C A:Val65 4.80 interactive model: