Manganese in the structure of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With The Inhibitor Beta-Thujaplicinol Bound At the Active Site (pdb 3k2p)

The binding sites of Manganese atom in the structure of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With The Inhibitor Beta-Thujaplicinol Bound At the Active Site (pdb code 3k2p). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 3k2p structure was solved by T.A.PAULY, D.M.HIMMEL, K.MAEGLEY, E.ARNOLD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 44.3-2.0 Space group P31 a (A) 51.143 b (A) 51.143 c (A) 112.435 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 22.6 Rfree (%) 24.1 Manganese Binding Sites: Manganese binding site 1 out of 4 in 3k2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3k2p. 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: Asp443, A: Gly444, A: Glu478, A: Asp498, A: Mn902, A: Jth1001, A: Hoh1, A: Hoh159, A: Hoh217, conact list: Atom Atom Distance (A) Mn CB A:Asp443 4.61 Mn OD2 A:Asp443 3.69 Mn OD1 A:Asp443 2.28 Mn CG A:Asp443 3.33 Mn CA A:Asp443 4.80 Mn O A:Gly444 4.07 Mn N A:Gly444 4.56 Mn OE1 A:Glu478 3.52 Mn OE2 A:Glu478 1.82 Mn CD A:Glu478 2.96 Mn CG A:Glu478 4.20 Mn O A:Asp498 4.91 Mn CB A:Asp498 4.46 Mn OD2 A:Asp498 3.20 Mn C A:Asp498 4.81 Mn OD1 A:Asp498 2.11 Mn CG A:Asp498 3.00 Mn MN A:Mn902 3.74 Mn C6 A:Jth1001 4.30 Mn O2 A:Jth1001 4.70 Mn C7 A:Jth1001 3.03 Mn C1 A:Jth1001 2.95 Mn O1 A:Jth1001 2.04 Mn O7 A:Jth1001 2.22 Mn C2 A:Jth1001 4.21 Mn O A:Hoh1 3.82 Mn O A:Hoh159 4.15 Mn O A:Hoh217 4.17 interactive model: Manganese binding site 2 out of 4 in 3k2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3k2p. 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: Asp443, A: Gly444, A: Asp498, A: His539, A: Asp549, A: Arg557, A: Mn901, A: Jth1001, A: Hoh126, A: Hoh131, conact list: Atom Atom Distance (A) Mn CB A:Asp443 4.61 Mn OD2 A:Asp443 2.24 Mn OD1 A:Asp443 3.54 Mn CG A:Asp443 3.24 Mn O A:Gly444 4.17 Mn OD2 A:Asp498 4.13 Mn CG A:Asp498 5.00 Mn NE2 A:His539 3.89 Mn CD2 A:His539 4.82 Mn CE1 A:His539 4.40 Mn O A:Asp549 4.85 Mn CB A:Asp549 3.62 Mn OD2 A:Asp549 2.15 Mn C A:Asp549 4.91 Mn OD1 A:Asp549 4.30 Mn CG A:Asp549 3.20 Mn CA A:Asp549 4.10 Mn CZ A:Arg557 4.31 Mn NH2 A:Arg557 3.25 Mn NH1 A:Arg557 4.51 Mn MN A:Mn901 3.74 Mn O2 A:Jth1001 2.18 Mn C7 A:Jth1001 4.26 Mn C1 A:Jth1001 2.96 Mn O1 A:Jth1001 2.26 Mn C3 A:Jth1001 4.21 Mn O7 A:Jth1001 4.68 Mn C2 A:Jth1001 2.95 Mn O A:Hoh126 4.93 Mn O A:Hoh131 4.51 interactive model: Manganese binding site 3 out of 4 in 3k2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3k2p. 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: Asp443, B: Gly444, B: Glu478, B: Asp498, B: Ser499, B: Ala538, B: Mn902, B: Jth1001, B: Hoh132, conact list: Atom Atom Distance (A) Mn CB B:Asp443 4.66 Mn OD2 B:Asp443 3.70 Mn OD1 B:Asp443 2.39 Mn CG B:Asp443 3.37 Mn CA B:Asp443 4.90 Mn O B:Gly444 4.10 Mn N B:Gly444 4.56 Mn OE1 B:Glu478 3.36 Mn OE2 B:Glu478 1.91 Mn CD B:Glu478 2.95 Mn CG B:Glu478 4.26 Mn O B:Asp498 4.87 Mn CB B:Asp498 4.38 Mn OD2 B:Asp498 3.20 Mn C B:Asp498 4.71 Mn OD1 B:Asp498 2.12 Mn CG B:Asp498 2.98 Mn CA B:Asp498 4.96 Mn N B:Ser499 4.86 Mn CB B:Ala538 4.95 Mn MN B:Mn902 3.76 Mn C6 B:Jth1001 4.35 Mn O2 B:Jth1001 4.99 Mn C7 B:Jth1001 3.10 Mn C1 B:Jth1001 3.13 Mn O1 B:Jth1001 2.32 Mn O7 B:Jth1001 2.29 Mn C2 B:Jth1001 4.42 Mn O B:Hoh132 4.09 interactive model: Manganese binding site 4 out of 4 in 3k2p Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 3k2p. 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: Asp443, B: Gly444, B: Asp498, B: Ala538, B: His539, B: Asp549, B: Arg557, B: Mn901, B: Jth1001, B: Hoh2, conact list: Atom Atom Distance (A) Mn CB B:Asp443 4.54 Mn OD2 B:Asp443 2.24 Mn OD1 B:Asp443 3.58 Mn CG B:Asp443 3.23 Mn O B:Gly444 4.10 Mn OD2 B:Asp498 4.21 Mn CB B:Ala538 4.99 Mn NE2 B:His539 3.79 Mn CD2 B:His539 4.70 Mn CE1 B:His539 4.35 Mn CB B:Asp549 3.57 Mn OD2 B:Asp549 2.20 Mn OD1 B:Asp549 4.23 Mn CG B:Asp549 3.16 Mn CA B:Asp549 4.08 Mn CZ B:Arg557 4.87 Mn NH2 B:Arg557 3.58 Mn MN B:Mn901 3.76 Mn O2 B:Jth1001 2.54 Mn C7 B:Jth1001 4.31 Mn C1 B:Jth1001 3.05 Mn O1 B:Jth1001 2.18 Mn C3 B:Jth1001 4.50 Mn O7 B:Jth1001 4.74 Mn C2 B:Jth1001 3.18 Mn O B:Hoh2 4.31 interactive model: