Potassium in PDB 3cdm: Structural Adaptation and Conservation in Quadruplex-Drug Recognition

The structure of Structural Adaptation and Conservation in Quadruplex-Drug Recognition, PDB code: 3cdm was solved by G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.575, 43.084, 56.937, 90.00, 103.58, 90.00
R / Rfree (%)	23.4 / 29.5

The binding sites of Potassium atom in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition (pdb code 3cdm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition, PDB code: 3cdm:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structural Adaptation and Conservation in Quadruplex-Drug Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:K24 b:18.3 occ:1.00 O6 A:DG23 2.7 18.1 1.0 O6 A:DG17 2.7 23.7 1.0 O6 A:DG5 2.7 18.1 1.0 O6 A:DG11 2.8 15.0 1.0 O6 A:DG16 2.9 20.9 1.0 O6 A:DG4 2.9 19.3 1.0 O6 A:DG10 2.9 7.4 1.0 O6 A:DG22 3.0 14.9 1.0 K A:K25 3.6 16.3 1.0 C6 A:DG11 3.6 7.8 1.0 C6 A:DG23 3.6 12.6 1.0 C6 A:DG5 3.6 12.7 1.0 C6 A:DG10 3.7 6.5 1.0 C6 A:DG17 3.7 13.7 1.0 C6 A:DG16 3.7 17.3 1.0 C6 A:DG22 3.7 12.3 1.0 C6 A:DG4 3.7 10.6 1.0 N1 A:DG11 3.8 11.8 1.0 N1 A:DG5 3.9 6.5 1.0 N1 A:DG17 3.9 15.2 1.0 N1 A:DG23 3.9 14.0 1.0 N1 A:DG10 3.9 9.6 1.0 N1 A:DG16 4.0 16.7 1.0 N1 A:DG4 4.0 13.6 1.0 N1 A:DG22 4.0 14.5 1.0 C4 A:NII26 4.8 15.3 1.0 C3 A:NII26 4.8 16.9 1.0 C5 A:DG10 4.8 10.1 1.0 C5 A:DG22 4.9 14.2 1.0 C5 A:DG4 4.9 16.3 1.0 C5 A:DG23 4.9 15.4 1.0 C5 A:DG11 4.9 14.2 1.0 C5 A:DG16 4.9 15.9 1.0 C5 A:DG5 5.0 13.2 1.0

Potassium binding site 2 out of 4 in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structural Adaptation and Conservation in Quadruplex-Drug Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:K25 b:16.3 occ:1.00 O6 A:DG21 2.7 13.8 1.0 O6 A:DG15 2.7 11.3 1.0 O6 A:DG9 2.8 13.4 1.0 O6 A:DG3 2.8 14.6 1.0 O6 A:DG10 3.0 7.4 1.0 O6 A:DG16 3.0 20.9 1.0 O6 A:DG22 3.0 14.9 1.0 O6 A:DG4 3.0 19.3 1.0 C6 A:DG9 3.5 12.5 1.0 C6 A:DG21 3.6 11.0 1.0 C6 A:DG15 3.6 14.3 1.0 K A:K24 3.6 18.3 1.0 C6 A:DG3 3.7 10.5 1.0 N1 A:DG9 3.7 12.0 1.0 N1 A:DG15 3.8 10.0 1.0 C6 A:DG10 3.8 6.5 1.0 N1 A:DG3 3.8 9.8 1.0 N1 A:DG21 3.8 9.5 1.0 C6 A:DG22 3.8 12.3 1.0 C6 A:DG16 3.9 17.3 1.0 C6 A:DG4 3.9 10.6 1.0 N1 A:DG22 4.1 14.5 1.0 N1 A:DG10 4.1 9.6 1.0 N1 A:DG4 4.1 13.6 1.0 N1 A:DG16 4.2 16.7 1.0 C4 A:NII27 4.6 22.6 1.0 C5 A:DG9 4.8 10.8 1.0 C3 A:NII27 4.8 25.2 1.0 C5 A:DG21 4.8 7.5 1.0 C5 A:DG15 4.8 14.7 1.0 C5 A:NII27 4.9 22.3 1.0 C5 A:DG3 4.9 11.9 1.0 C7 A:NII27 4.9 24.7 1.0

Potassium binding site 3 out of 4 in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structural Adaptation and Conservation in Quadruplex-Drug Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:K24 b:16.7 occ:1.00 O6 B:DG11 2.6 16.1 1.0 O6 B:DG5 2.6 11.5 1.0 O6 B:DG23 2.7 13.8 1.0 O6 B:DG17 2.7 15.3 1.0 O6 B:DG4 3.0 13.4 1.0 O6 B:DG10 3.0 17.4 1.0 O6 B:DG16 3.1 17.1 1.0 O6 B:DG22 3.1 14.7 1.0 C6 B:DG23 3.6 13.1 1.0 C6 B:DG5 3.6 11.0 1.0 C6 B:DG17 3.6 7.5 1.0 C6 B:DG11 3.6 15.8 1.0 K B:K25 3.7 13.2 1.0 N1 B:DG23 3.7 15.1 1.0 C6 B:DG4 3.8 8.2 1.0 N1 B:DG17 3.8 8.3 1.0 C6 B:DG16 3.8 12.5 1.0 C6 B:DG10 3.8 15.0 1.0 C6 B:DG22 3.8 11.6 1.0 N1 B:DG11 3.9 16.1 1.0 N1 B:DG5 3.9 10.6 1.0 N1 B:DG4 4.0 9.2 1.0 N1 B:DG16 4.0 10.7 1.0 N1 B:DG22 4.1 14.0 1.0 N1 B:DG10 4.1 16.2 1.0 C5 B:NII26 4.7 19.3 1.0 C10 B:NII26 4.8 21.3 1.0 C5 B:DG5 4.9 9.3 1.0 C5 B:DG23 4.9 13.0 1.0 C5 B:DG4 4.9 10.3 1.0 C5 B:DG16 4.9 11.3 1.0 C5 B:DG17 4.9 14.8 1.0 C6 B:NII26 4.9 23.7 1.0 C5 B:DG10 4.9 15.6 1.0 C5 B:DG11 4.9 16.0 1.0 C5 B:DG22 4.9 14.2 1.0 C11 B:NII26 5.0 23.3 1.0

Potassium binding site 4 out of 4 in the Structural Adaptation and Conservation in Quadruplex-Drug Recognition


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structural Adaptation and Conservation in Quadruplex-Drug Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:K25 b:13.2 occ:1.00 O6 B:DG9 2.7 9.8 1.0 O6 B:DG3 2.8 15.8 1.0 O6 B:DG4 2.9 13.4 1.0 O6 B:DG15 2.9 20.0 1.0 O6 B:DG21 2.9 13.4 1.0 O6 B:DG10 2.9 17.4 1.0 O6 B:DG16 2.9 17.1 1.0 O6 B:DG22 3.0 14.7 1.0 C6 B:DG9 3.6 11.6 1.0 C6 B:DG3 3.6 13.7 1.0 C6 B:DG21 3.7 9.5 1.0 C6 B:DG4 3.7 8.2 1.0 K B:K24 3.7 16.7 1.0 C6 B:DG15 3.7 11.9 1.0 N1 B:DG3 3.8 13.2 1.0 C6 B:DG16 3.8 12.5 1.0 C6 B:DG10 3.8 15.0 1.0 N1 B:DG4 3.9 9.2 1.0 C6 B:DG22 3.9 11.6 1.0 N1 B:DG9 3.9 8.9 1.0 N1 B:DG21 3.9 10.8 1.0 N1 B:DG15 3.9 8.6 1.0 N1 B:DG16 4.1 10.7 1.0 N1 B:DG10 4.1 16.2 1.0 N1 B:DG22 4.2 14.0 1.0 C5 B:NII27 4.7 27.6 1.0 C10 B:NII27 4.7 28.3 1.0 C5 B:DG9 4.8 11.5 1.0 C5 B:DG3 4.8 14.1 1.0 C5 B:DG21 4.9 12.7 1.0 C5 B:DG4 4.9 10.3 1.0 C5 B:DG15 4.9 11.2 1.0 C6 B:NII27 5.0 28.7 1.0 C4 B:NII27 5.0 31.4 1.0

G.N.Parkinson, F.Cuenca, S.Neidle. Topology Conservation and Loop Flexibility in Quadruplex-Drug Recognition: Crystal Structures of Inter- and Intramolecular Telomeric Dna Quadruplex-Drug Complexes J.Mol.Biol. V. 381 1145 2008.
ISSN: ISSN 0022-2836
PubMed: 18619463
DOI: 10.1016/J.JMB.2008.06.022