Manganese in the structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, At 3.0 A Resolution. (pdb 4e7l)

The binding sites of Manganese atom in the structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, At 3.0 A Resolution. (pdb code 4e7l). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 4e7l structure was solved by G.N.MAERTENS, P.CHEREPANOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.0-3.0 Space group P41212 a (A) 159.078 b (A) 159.078 c (A) 126.814 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.8 Rfree (%) 26.4 Manganese Binding Sites: Manganese binding site 1 out of 3 in 4e7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 4e7l. 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: Asp128, A: Tyr129, A: Asp185, A: Glu221, A: Asn224, D: Da17, t: Dg-1, T: Dc0, A: Mn403, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.56 Mn OD2 A:Asp128 2.48 Mn OD1 A:Asp128 2.98 Mn CG A:Asp128 3.08 Mn O A:Tyr129 4.04 Mn OD1 A:Asp185 4.22 Mn OE1 A:Glu221 2.60 Mn OE2 A:Glu221 2.60 Mn CD A:Glu221 2.92 Mn CG A:Glu221 4.37 Mn ND2 A:Asn224 4.26 Mn OP1 D:Da17 4.77 Mn C3' D:Da17 3.86 Mn C1' D:Da17 4.76 Mn O3' D:Da17 2.76 Mn O4' D:Da17 4.91 Mn C5' D:Da17 4.86 Mn C2' D:Da17 4.47 Mn C4' D:Da17 3.94 Mn O3' t:Dg-1 4.04 Mn OP1 T:Dc0 3.08 Mn P T:Dc0 3.55 Mn OP2 T:Dc0 4.73 Mn C5' T:Dc0 4.20 Mn O5' T:Dc0 4.43 Mn MN A:Mn403 3.02 interactive model: Manganese binding site 2 out of 3 in 4e7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 4e7l. 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: Asp128, A: Tyr129, A: Asp185, A: Glu221, D: Da17, t: Dg-1, T: Dc0, A: Mn402, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.76 Mn OD2 A:Asp128 3.75 Mn OD1 A:Asp128 2.70 Mn CG A:Asp128 3.50 Mn CA A:Asp128 4.90 Mn O A:Tyr129 3.94 Mn N A:Tyr129 4.07 Mn CB A:Tyr129 4.84 Mn C A:Tyr129 4.79 Mn CA A:Tyr129 4.78 Mn CB A:Asp185 4.76 Mn OD2 A:Asp185 3.93 Mn OD1 A:Asp185 2.43 Mn CG A:Asp185 3.51 Mn OE2 A:Glu221 4.94 Mn O3' D:Da17 4.67 Mn C3' t:Dg-1 3.71 Mn C1' t:Dg-1 4.96 Mn O3' t:Dg-1 2.55 Mn C2' t:Dg-1 4.24 Mn C4' t:Dg-1 4.03 Mn OP1 T:Dc0 2.97 Mn P T:Dc0 4.35 Mn C5' T:Dc0 4.87 Mn MN A:Mn402 3.02 interactive model: Manganese binding site 3 out of 3 in 4e7l Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 4e7l. 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: Asp128, B: Tyr129, B: Asp185, B: Phe190, conact list: Atom Atom Distance (A) Mn CB B:Asp128 4.10 Mn OD2 B:Asp128 2.37 Mn C B:Asp128 4.97 Mn OD1 B:Asp128 2.38 Mn CG B:Asp128 2.67 Mn CA B:Asp128 4.63 Mn O B:Tyr129 4.33 Mn N B:Tyr129 4.21 Mn CB B:Asp185 4.96 Mn OD2 B:Asp185 3.45 Mn OD1 B:Asp185 2.71 Mn CG B:Asp185 3.48 Mn CE2 B:Phe190 4.91 interactive model: