Potassium in PDB 3nyp: 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

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 was solved by N.H.Campbell, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.99 / 1.18
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.800, 44.460, 28.140, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.8

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 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Potassium atom in the 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 within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the 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:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:K14 b:6.4 occ:1.00 O6 A:DG1 2.9 7.7 1.0 O6 A:DG11 3.0 6.8 1.0 O6 A:DG12 3.0 7.5 1.0 O6 B:DG3 3.0 6.1 1.0 O6 B:DG10 3.1 7.2 1.0 O6 B:DG4 3.1 8.6 1.0 O6 A:DG2 3.1 7.9 1.0 O6 B:DG9 3.1 8.5 1.0 K A:K15 3.5 5.5 1.0 K B:K13 3.6 7.8 1.0 C6 A:DG11 3.8 5.7 1.0 C6 B:DG3 3.8 8.6 1.0 C6 A:DG1 3.9 8.5 1.0 C6 B:DG10 4.0 8.5 1.0 C6 B:DG9 4.0 7.3 1.0 C6 A:DG12 4.0 8.7 1.0 C6 B:DG4 4.0 7.3 1.0 N1 A:DG11 4.0 6.5 1.0 C6 A:DG2 4.0 6.3 1.0 N1 B:DG3 4.1 6.8 1.0 N1 A:DG1 4.2 7.6 1.0 N1 B:DG4 4.2 8.8 1.0 N1 B:DG10 4.2 7.2 1.0 N1 A:DG12 4.3 7.9 1.0 N1 B:DG9 4.3 7.8 1.0 N1 A:DG2 4.3 6.8 1.0 C5 A:DG11 4.9 6.1 1.0

Potassium binding site 2 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:K15 b:5.5 occ:1.00 O6 B:DG2 2.9 6.3 1.0 O6 A:DG10 3.0 6.8 1.0 O6 B:DG11 3.0 6.0 1.0 O6 A:DG2 3.0 7.9 1.0 O6 B:DG3 3.0 6.1 1.0 O6 A:DG3 3.0 7.2 1.0 O6 B:DG10 3.1 7.2 1.0 O6 A:DG11 3.1 6.8 1.0 K A:K14 3.5 6.4 1.0 K A:K16 3.7 5.8 1.0 C6 B:DG2 3.8 6.0 1.0 C6 A:DG2 3.8 6.3 1.0 C6 A:DG10 3.9 6.3 1.0 C6 B:DG11 3.9 7.0 1.0 C6 B:DG10 4.0 8.5 1.0 C6 A:DG3 4.0 6.7 1.0 C6 B:DG3 4.0 8.6 1.0 C6 A:DG11 4.1 5.7 1.0 N1 B:DG2 4.1 5.9 1.0 N1 A:DG2 4.1 6.8 1.0 N1 A:DG10 4.1 6.7 1.0 N1 B:DG11 4.2 6.1 1.0 N1 B:DG10 4.2 7.2 1.0 N1 A:DG3 4.3 7.5 1.0 N1 A:DG11 4.3 6.5 1.0 N1 B:DG3 4.4 6.8 1.0 C5 B:DG2 5.0 5.7 1.0

Potassium binding site 3 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:K16 b:5.8 occ:1.00 O6 B:DG12 2.9 8.0 1.0 O6 A:DG9 2.9 7.0 1.0 O6 A:DG4 2.9 7.2 1.0 O6 B:DG1 2.9 6.3 1.0 O6 B:DG2 3.1 6.3 1.0 O6 A:DG3 3.2 7.2 1.0 O6 B:DG11 3.2 6.0 1.0 O6 A:DG10 3.2 6.8 1.0 K A:K15 3.7 5.5 1.0 C6 B:DG12 3.8 6.8 1.0 C6 A:DG9 3.8 6.3 1.0 C6 B:DG1 3.9 7.3 1.0 C6 A:DG4 3.9 6.9 1.0 C6 B:DG2 4.0 6.0 1.0 C6 A:DG3 4.0 6.7 1.0 C6 B:DG11 4.0 7.0 1.0 N1 B:DG12 4.1 7.6 1.0 N1 A:DG9 4.1 7.5 1.0 N1 B:DG1 4.1 8.0 1.0 C6 A:DG10 4.1 6.3 1.0 N1 A:DG4 4.1 6.8 1.0 N1 B:DG2 4.2 5.9 1.0 N1 A:DG3 4.3 7.5 1.0 N1 B:DG11 4.3 6.1 1.0 N1 A:DG10 4.4 6.7 1.0 O2 A:DT6 4.6 8.6 1.0

Potassium binding site 4 out of 4 in the 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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 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 within 5.0Å range: probe atom residue distance (Å) B Occ B:K13 b:7.8 occ:1.00 O2 B:DT7 2.8 8.7 1.0 O B:HOH14 2.9 10.4 1.0 O2 B:DT5 3.0 7.5 1.0 O6 A:DG12 3.0 7.5 1.0 O6 B:DG4 3.1 8.6 1.0 O6 B:DG9 3.1 8.5 1.0 O B:HOH24 3.2 10.2 1.0 O6 A:DG1 3.2 7.7 1.0 K A:K14 3.6 6.4 1.0 C2 B:DT7 3.7 10.4 1.0 C6 A:DG12 3.8 8.7 1.0 C2 B:DT5 3.9 9.7 1.0 N3 B:DT7 3.9 8.5 1.0 C6 B:DG4 3.9 7.3 1.0 C6 B:DG9 4.0 7.3 1.0 C6 A:DG1 4.0 8.5 1.0 N1 A:DG12 4.1 7.9 1.0 N3 B:DT5 4.1 7.5 1.0 N1 B:DG9 4.2 7.8 1.0 N1 A:DG1 4.3 7.6 1.0 N1 B:DG4 4.3 8.8 1.0 O2 B:DT6 4.6 11.8 1.0 C5 A:DG12 4.9 8.4 1.0 N1 B:DT7 5.0 11.3 1.0 C5 B:DG4 5.0 6.8 1.0

N.H.Campbell, D.L.Smith, A.P.Reszka, S.Neidle, D.O'hagan. Fluorine in Medicinal Chemistry: Beta-Fluorination of Peripheral Pyrrolidines Attached to Acridine Ligands Affects Their Interactions with G-Quadruplex Dna. Org.Biomol.Chem. V. 9 1328 2011.
ISSN: ISSN 1477-0520
PubMed: 21221451
DOI: 10.1039/C0OB00886A