Manganese in the structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex With Manganese and GS9137 (Elvitegravir) (pdb 3l2w)

The binding sites of Manganese atom in the structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex With Manganese and GS9137 (Elvitegravir) (pdb code 3l2w). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3l2w structure was solved by S.HARE, S.S.GUPTA, P.CHEREPANOV, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 35.9-3.2 Space group P41212 a (A) 157.880 b (A) 157.880 c (A) 125.090 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 22 Manganese Binding Sites: Manganese binding site 1 out of 3 in 3l2w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3l2w. 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: Phe190, A: Mn395, A: Elv397, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.33 Mn OD2 A:Asp128 3.57 Mn C A:Asp128 4.89 Mn OD1 A:Asp128 1.95 Mn CG A:Asp128 3.07 Mn CA A:Asp128 4.58 Mn O A:Tyr129 4.04 Mn N A:Tyr129 4.11 Mn C A:Tyr129 4.93 Mn CA A:Tyr129 4.94 Mn CB A:Asp185 4.64 Mn OD2 A:Asp185 3.25 Mn OD1 A:Asp185 2.35 Mn CG A:Asp185 3.17 Mn CE2 A:Phe190 4.94 Mn MN A:Mn395 4.23 Mn OAD A:Elv397 2.56 Mn CAY A:Elv397 4.15 Mn CAO A:Elv397 4.73 Mn OAG A:Elv397 2.14 Mn CAS A:Elv397 2.66 interactive model: Manganese binding site 2 out of 3 in 3l2w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3l2w. 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, A: Mn394, A: Elv397, conact list: Atom Atom Distance (A) Mn CB A:Asp128 4.35 Mn OD2 A:Asp128 2.06 Mn OD1 A:Asp128 3.65 Mn CG A:Asp128 3.14 Mn O A:Tyr129 4.14 Mn OD1 A:Asp185 4.83 Mn OE1 A:Glu221 2.22 Mn CB A:Glu221 4.97 Mn OE2 A:Glu221 2.35 Mn CD A:Glu221 2.62 Mn CG A:Glu221 4.13 Mn ND2 A:Asn224 3.57 Mn CG A:Asn224 4.84 Mn O3' D:Dc16 4.46 Mn C2' D:Dc16 4.95 Mn OP1 D:Da17 4.03 Mn P D:Da17 4.83 Mn MN A:Mn394 4.23 Mn CBA A:Elv397 4.49 Mn CAZ A:Elv397 3.18 Mn OAD A:Elv397 1.99 Mn CAY A:Elv397 3.48 Mn OAE A:Elv397 2.21 Mn CAO A:Elv397 4.85 Mn OAG A:Elv397 4.08 Mn CAS A:Elv397 3.01 Mn CAM A:Elv397 4.99 interactive model: Manganese binding site 3 out of 3 in 3l2w Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3l2w. 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, conact list: Atom Atom Distance (A) Mn CB B:Asp128 4.66 Mn OD2 B:Asp128 3.30 Mn OD1 B:Asp128 2.44 Mn CG B:Asp128 3.23 Mn O B:Tyr129 4.19 Mn N B:Tyr129 4.30 Mn CB B:Tyr129 4.98 Mn CA B:Tyr129 4.98 Mn CB B:Asp185 4.64 Mn OD2 B:Asp185 3.32 Mn OD1 B:Asp185 2.38 Mn CG B:Asp185 3.22 interactive model: