Potassium in the structure of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex With A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains (pdb 3nyp)

The binding sites of Potassium atom in the structure of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex With A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains (pdb code 3nyp). This binding sites where shown with 5.0 Angstroms radius around Potassium atom. The 3nyp structure was solved by N.H.CAMPBELL, S.NEIDLE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.0-1.2 Space group P21212 a (A) 57.800 b (A) 44.460 c (A) 28.140 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.5 Rfree (%) 18.8 Potassium Binding Sites: Potassium binding site 1 out of 4 in 3nyp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Potassium in the PDB 3nyp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg1, A: Dg2, A: Dg11, A: Dg12, B: Dg3, B: Dg4, B: Dg9, B: Dg10, A: K15, B: K13, conact list: Atom Atom Distance (A) K C6 A:Dg1 3.85 K N1 A:Dg1 4.18 K O6 A:Dg1 2.93 K C6 A:Dg2 4.05 K N1 A:Dg2 4.33 K O6 A:Dg2 3.08 K C6 A:Dg11 3.77 K N1 A:Dg11 4.05 K C5 A:Dg11 4.94 K O6 A:Dg11 2.98 K C6 A:Dg12 3.99 K N1 A:Dg12 4.27 K O6 A:Dg12 3.02 K C6 B:Dg3 3.84 K N1 B:Dg3 4.14 K O6 B:Dg3 3.04 K C6 B:Dg4 4.04 K N1 B:Dg4 4.23 K O6 B:Dg4 3.07 K C6 B:Dg9 3.98 K N1 B:Dg9 4.27 K O6 B:Dg9 3.08 K C6 B:Dg10 3.96 K N1 B:Dg10 4.24 K O6 B:Dg10 3.06 K K A:K15 3.53 K K B:K13 3.63 interactive model: Potassium binding site 2 out of 4 in 3nyp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Potassium in the PDB 3nyp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg2, A: Dg3, A: Dg10, A: Dg11, B: Dg2, B: Dg3, B: Dg10, B: Dg11, A: K14, A: K16, conact list: Atom Atom Distance (A) K C6 A:Dg2 3.83 K N1 A:Dg2 4.11 K O6 A:Dg2 3.00 K C6 A:Dg3 4.02 K N1 A:Dg3 4.29 K O6 A:Dg3 3.03 K C6 A:Dg10 3.88 K N1 A:Dg10 4.14 K O6 A:Dg10 2.99 K C6 A:Dg11 4.08 K N1 A:Dg11 4.33 K O6 A:Dg11 3.12 K C6 B:Dg2 3.78 K N1 B:Dg2 4.09 K C5 B:Dg2 4.97 K O6 B:Dg2 2.93 K C6 B:Dg3 4.03 K N1 B:Dg3 4.39 K O6 B:Dg3 3.02 K C6 B:Dg10 3.99 K N1 B:Dg10 4.25 K O6 B:Dg10 3.12 K C6 B:Dg11 3.92 K N1 B:Dg11 4.20 K O6 B:Dg11 3.00 K K A:K14 3.53 K K A:K16 3.70 interactive model: Potassium binding site 3 out of 4 in 3nyp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Potassium in the PDB 3nyp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg3, A: Dg4, A: Dt6, A: Dg9, A: Dg10, B: Dg1, B: Dg2, B: Dg11, B: Dg12, A: K15, conact list: Atom Atom Distance (A) K C6 A:Dg3 3.99 K N1 A:Dg3 4.27 K O6 A:Dg3 3.21 K C6 A:Dg4 3.91 K N1 A:Dg4 4.15 K O6 A:Dg4 2.93 K O2 A:Dt6 4.60 K C6 A:Dg9 3.84 K N1 A:Dg9 4.08 K O6 A:Dg9 2.90 K C6 A:Dg10 4.11 K N1 A:Dg10 4.36 K O6 A:Dg10 3.25 K C6 B:Dg1 3.85 K N1 B:Dg1 4.10 K O6 B:Dg1 2.93 K C6 B:Dg2 3.97 K N1 B:Dg2 4.20 K O6 B:Dg2 3.10 K C6 B:Dg11 4.05 K N1 B:Dg11 4.31 K O6 B:Dg11 3.22 K C6 B:Dg12 3.82 K N1 B:Dg12 4.08 K O6 B:Dg12 2.89 K K A:K15 3.70 interactive model: Potassium binding site 4 out of 4 in 3nyp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Potassium in the PDB 3nyp. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg1, A: Dg12, B: Dg4, B: Dt5, B: Dt6, B: Dt7, B: Dg9, A: K14, B: Hoh14, B: Hoh24, conact list: Atom Atom Distance (A) K C6 A:Dg1 4.04 K N1 A:Dg1 4.28 K O6 A:Dg1 3.22 K C6 A:Dg12 3.77 K N1 A:Dg12 4.06 K C5 A:Dg12 4.90 K O6 A:Dg12 3.02 K C6 B:Dg4 3.94 K N1 B:Dg4 4.33 K C5 B:Dg4 4.98 K O6 B:Dg4 3.13 K N3 B:Dt5 4.07 K C2 B:Dt5 3.92 K O2 B:Dt5 3.00 K O2 B:Dt6 4.58 K N3 B:Dt7 3.93 K C2 B:Dt7 3.72 K N1 B:Dt7 4.95 K O2 B:Dt7 2.82 K C6 B:Dg9 3.97 K N1 B:Dg9 4.15 K O6 B:Dg9 3.14 K K A:K14 3.63 K O B:Hoh14 2.91 K O B:Hoh24 3.17 interactive model: