Manganese in the structure of Structure Of The N-Terminal Exonuclease Domain Of the Epsilon Subunit of E.Coli Dna Polymerase III At pH 8.5 (pdb 1j53)

The binding sites of Manganese atom in the structure of Structure Of The N-Terminal Exonuclease Domain Of the Epsilon Subunit of E.Coli Dna Polymerase III At pH 8.5 (pdb code 1j53). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 1j53 structure was solved by S.HAMDAN, P.D.CARR, S.E.BROWN, D.L.OLLIS, N.E.DIXON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.8 Space group P41212 a (A) 60.800 b (A) 60.800 c (A) 111.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 22.7 Manganese Binding Sites: Manganese binding site 1 out of 2 in 1j53 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 1j53. 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: Asp12, A: Thr13, A: Glu14, A: Arg159, A: His162, A: Gly163, A: Ala164, A: Asp167, A: Mn3001, A: Tmp2000, A: Hoh5002, A: Hoh5145, A: Hoh5146, conact list: Atom Atom Distance (A) Mn CB A:Asp12 4.52 Mn OD2 A:Asp12 2.14 Mn OD1 A:Asp12 3.59 Mn CG A:Asp12 3.20 Mn O A:Thr13 3.87 Mn N A:Thr13 5.00 Mn C A:Thr13 4.67 Mn OE1 A:Glu14 3.30 Mn OE2 A:Glu14 2.02 Mn CD A:Glu14 2.96 Mn CG A:Glu14 4.29 Mn NH2 A:Arg159 4.53 Mn CB A:His162 4.07 Mn ND1 A:His162 4.71 Mn C A:His162 4.89 Mn CG A:His162 4.81 Mn O A:Gly163 4.04 Mn N A:Gly163 4.53 Mn C A:Gly163 4.28 Mn CA A:Gly163 4.96 Mn N A:Ala164 4.54 Mn CA A:Ala164 4.56 Mn CB A:Asp167 3.63 Mn OD2 A:Asp167 2.08 Mn OD1 A:Asp167 4.18 Mn CG A:Asp167 3.13 Mn MN A:Mn3001 3.73 Mn P A:Tmp2000 3.41 Mn O3P A:Tmp2000 1.95 Mn C5' A:Tmp2000 4.07 Mn O1P A:Tmp2000 4.58 Mn O5' A:Tmp2000 4.35 Mn O2P A:Tmp2000 3.87 Mn O A:Hoh5002 2.37 Mn O A:Hoh5145 4.11 Mn O A:Hoh5146 4.42 interactive model: Manganese binding site 2 out of 2 in 1j53 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 1j53. 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: Asp12, A: Thr13, A: His98, A: Phe102, A: Asp103, A: Asp167, A: Mn3000, A: Tmp2000, A: Tmp2100, A: Hoh5013, A: Hoh5017, A: Hoh5040, A: Hoh5145, A: Hoh5146, conact list: Atom Atom Distance (A) Mn CB A:Asp12 4.40 Mn OD2 A:Asp12 3.50 Mn OD1 A:Asp12 2.04 Mn CG A:Asp12 3.10 Mn CA A:Asp12 4.80 Mn O A:Thr13 4.12 Mn N A:Thr13 4.62 Mn O A:His98 4.50 Mn CD2 A:Phe102 4.97 Mn OD2 A:Asp103 4.07 Mn OD1 A:Asp103 4.20 Mn CG A:Asp103 4.58 Mn OD2 A:Asp167 4.90 Mn MN A:Mn3000 3.73 Mn P A:Tmp2000 2.78 Mn O3P A:Tmp2000 2.26 Mn C5' A:Tmp2000 4.17 Mn O1P A:Tmp2000 2.32 Mn O5' A:Tmp2000 3.72 Mn O2P A:Tmp2000 3.99 Mn O4' A:Tmp2100 4.81 Mn C4' A:Tmp2100 4.57 Mn O A:Hoh5013 4.12 Mn O A:Hoh5017 4.49 Mn O A:Hoh5040 2.15 Mn O A:Hoh5145 2.23 Mn O A:Hoh5146 2.18 interactive model: