Manganese in the structure of Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, At 3.0 A Resolution (pdb 4e7k)

The binding sites of Manganese atom in the structure of Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, At 3.0 A Resolution (pdb code 4e7k). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 4e7k 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) 163.914 b (A) 163.914 c (A) 129.675 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.5 Rfree (%) 28.9 Manganese Binding Sites: Manganese binding site 1 out of 3 in 4e7k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 4e7k. 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: Dc16, D: Da17, T: Dg-1, T: Dc0, A: Mn403, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.49 Mn OD2 A:Asp128 2.32 Mn OD1 A:Asp128 3.09 Mn CG A:Asp128 3.05 Mn O A:Tyr129 3.59 Mn C A:Tyr129 4.74 Mn OD1 A:Asp185 4.97 Mn OE1 A:Glu221 2.47 Mn OE2 A:Glu221 2.52 Mn CD A:Glu221 2.83 Mn CG A:Glu221 4.35 Mn ND2 A:Asn224 3.70 Mn O3' D:Dc16 4.85 Mn OP1 D:Da17 4.08 Mn C3' D:Da17 3.78 Mn C1' D:Da17 4.97 Mn O3' D:Da17 2.56 Mn C5' D:Da17 4.73 Mn C2' D:Da17 4.80 Mn C4' D:Da17 3.97 Mn O3' T:Dg-1 4.71 Mn OP1 T:Dc0 2.36 Mn P T:Dc0 3.52 Mn OP2 T:Dc0 4.42 Mn C5' T:Dc0 4.54 Mn O5' T:Dc0 3.73 Mn MN A:Mn403 3.88 interactive model: Manganese binding site 2 out of 3 in 4e7k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 4e7k. 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 4.59 Mn OD2 A:Asp128 4.24 Mn C A:Asp128 4.96 Mn OD1 A:Asp128 2.37 Mn CG A:Asp128 3.56 Mn CA A:Asp128 4.74 Mn O A:Tyr129 4.47 Mn N A:Tyr129 4.15 Mn CA A:Tyr129 4.97 Mn CB A:Asp185 4.80 Mn OD2 A:Asp185 3.24 Mn OD1 A:Asp185 2.67 Mn CG A:Asp185 3.33 Mn OE2 A:Glu221 4.48 Mn O3' D:Da17 4.95 Mn C3' T:Dg-1 3.66 Mn O3' T:Dg-1 2.45 Mn C5' T:Dg-1 4.25 Mn C2' T:Dg-1 4.61 Mn C4' T:Dg-1 3.89 Mn OP1 T:Dc0 2.38 Mn P T:Dc0 2.94 Mn OP2 T:Dc0 4.27 Mn O5' T:Dc0 3.76 Mn MN A:Mn402 3.88 interactive model: Manganese binding site 3 out of 3 in 4e7k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 4e7k. 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, B: Hoh501, B: Hoh502, B: Hoh504, conact list: Atom Atom Distance (A) Mn CB B:Asp128 4.44 Mn OD2 B:Asp128 3.20 Mn C B:Asp128 4.81 Mn OD1 B:Asp128 2.61 Mn CG B:Asp128 3.13 Mn CA B:Asp128 4.71 Mn O B:Tyr129 4.04 Mn N B:Tyr129 3.93 Mn CB B:Tyr129 4.78 Mn C B:Tyr129 4.81 Mn CA B:Tyr129 4.70 Mn CB B:Asp185 4.71 Mn OD2 B:Asp185 3.75 Mn OD1 B:Asp185 2.37 Mn CG B:Asp185 3.41 Mn CE2 B:Phe190 4.92 Mn O B:Hoh501 2.66 Mn O B:Hoh502 2.56 Mn O B:Hoh504 2.57 interactive model: