Manganese in the structure of Human Foamy Virus Integrase - Catalytic Core. Manganese- Bound Structure. (pdb 2x6n)

The binding sites of Manganese atom in the structure of Human Foamy Virus Integrase - Catalytic Core. Manganese- Bound Structure. (pdb code 2x6n). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2x6n structure was solved by S.RETY, O.DELELIS, L.REZABKOVA, B.DUBANCHET, J.SILHAN, A.LEWIT-BENTLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 44.6-2.1 Space group P212121 a (A) 84.767 b (A) 89.232 c (A) 177.084 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.574 Rfree (%) 27.004 Manganese Binding Sites: Manganese binding site 1 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2x6n. 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: Hoh2006, A: Hoh2018, A: Hoh2039, A: Hoh2079, A: Hoh2080, A: Hoh2081, A: Hoh2082, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.57 Mn OD2 A:Asp128 3.48 Mn OD1 A:Asp128 2.22 Mn CG A:Asp128 3.19 Mn CA A:Asp128 4.88 Mn O A:Tyr129 4.32 Mn N A:Tyr129 4.41 Mn CB A:Asp185 4.53 Mn OD2 A:Asp185 2.19 Mn OD1 A:Asp185 3.39 Mn CG A:Asp185 3.14 Mn O A:Hoh2006 4.00 Mn O A:Hoh2018 4.23 Mn O A:Hoh2039 4.85 Mn O A:Hoh2079 2.18 Mn O A:Hoh2080 2.10 Mn O A:Hoh2081 2.29 Mn O A:Hoh2082 1.97 interactive model: Manganese binding site 2 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2x6n. 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, D: Lys262, D: Tyr263, B: Hoh2005, B: Hoh2006, B: Hoh2009, B: Hoh2075, D: Hoh2011, conact list: Atom Atom Distance (A) Mn CB B:Asp128 4.64 Mn OD2 B:Asp128 3.41 Mn OD1 B:Asp128 2.31 Mn CG B:Asp128 3.22 Mn O B:Tyr129 4.18 Mn N B:Tyr129 4.46 Mn CB B:Asp185 4.56 Mn OD2 B:Asp185 2.22 Mn OD1 B:Asp185 3.46 Mn CG B:Asp185 3.19 Mn CD D:Lys262 4.79 Mn OH D:Tyr263 4.20 Mn O B:Hoh2005 4.19 Mn O B:Hoh2006 4.74 Mn O B:Hoh2009 4.15 Mn O B:Hoh2075 2.30 Mn O D:Hoh2011 4.25 interactive model: Manganese binding site 3 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2x6n. 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: C: Asp128, C: Tyr129, C: Asp185, C: Hoh2006, C: Hoh2019, C: Hoh2044, C: Hoh2045, C: Hoh2046, C: Hoh2047, conact list: Atom Atom Distance (A) Mn CB C:Asp128 4.51 Mn OD2 C:Asp128 3.26 Mn OD1 C:Asp128 2.22 Mn CG C:Asp128 3.09 Mn CA C:Asp128 4.95 Mn O C:Tyr129 4.16 Mn N C:Tyr129 4.42 Mn CB C:Asp185 4.50 Mn OD2 C:Asp185 2.19 Mn OD1 C:Asp185 3.40 Mn CG C:Asp185 3.14 Mn O C:Hoh2006 4.17 Mn O C:Hoh2019 4.10 Mn O C:Hoh2044 2.09 Mn O C:Hoh2045 2.08 Mn O C:Hoh2046 2.87 Mn O C:Hoh2047 2.11 interactive model: Manganese binding site 4 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2x6n. 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: D: Asp128, D: Tyr129, D: Asp185, conact list: Atom Atom Distance (A) Mn CB D:Asp128 4.46 Mn OD2 D:Asp128 2.97 Mn OD1 D:Asp128 2.29 Mn CG D:Asp128 2.98 Mn O D:Tyr129 4.26 Mn N D:Tyr129 4.67 Mn CB D:Asp185 4.31 Mn OD2 D:Asp185 2.05 Mn OD1 D:Asp185 3.93 Mn CG D:Asp185 3.25 interactive model: Manganese binding site 5 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2x6n. 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: E: Asp128, E: Tyr129, E: Asp185, E: Hoh2003, E: Hoh2004, E: Hoh2007, E: Hoh2050, E: Hoh2051, E: Hoh2052, conact list: Atom Atom Distance (A) Mn CB E:Asp128 4.54 Mn OD2 E:Asp128 3.42 Mn OD1 E:Asp128 2.16 Mn CG E:Asp128 3.14 Mn CA E:Asp128 4.93 Mn O E:Tyr129 4.16 Mn N E:Tyr129 4.46 Mn CB E:Asp185 4.60 Mn OD2 E:Asp185 2.24 Mn OD1 E:Asp185 3.50 Mn CG E:Asp185 3.22 Mn O E:Hoh2003 4.07 Mn O E:Hoh2004 2.43 Mn O E:Hoh2007 4.44 Mn O E:Hoh2050 2.02 Mn O E:Hoh2051 2.16 Mn O E:Hoh2052 2.32 interactive model: Manganese binding site 6 out of 6 in 2x6n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2x6n. 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: F: Asp128, F: Tyr129, F: Asp185, F: Hoh2002, F: Hoh2006, F: Hoh2019, F: Hoh2033, F: Hoh2034, F: Hoh2035, F: Hoh2036, conact list: Atom Atom Distance (A) Mn CB F:Asp128 4.64 Mn OD2 F:Asp128 3.49 Mn OD1 F:Asp128 2.26 Mn CG F:Asp128 3.24 Mn O F:Tyr129 4.30 Mn N F:Tyr129 4.55 Mn CB F:Asp185 4.48 Mn OD2 F:Asp185 2.13 Mn OD1 F:Asp185 3.43 Mn CG F:Asp185 3.12 Mn O F:Hoh2002 4.19 Mn O F:Hoh2006 4.54 Mn O F:Hoh2019 4.64 Mn O F:Hoh2033 2.44 Mn O F:Hoh2034 2.08 Mn O F:Hoh2035 2.47 Mn O F:Hoh2036 2.25 interactive model: