Potassium in PDB 2avh: G4T3G4 Dimeric Quadruplex Structure

The structure of G4T3G4 Dimeric Quadruplex Structure, PDB code: 2avh was solved by P.Hazel, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.30 / 1.50
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	29.932, 37.112, 43.653, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 20.8

The binding sites of Potassium atom in the G4T3G4 Dimeric Quadruplex Structure (pdb code 2avh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the G4T3G4 Dimeric Quadruplex Structure, PDB code: 2avh:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the G4T3G4 Dimeric Quadruplex Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of G4T3G4 Dimeric Quadruplex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K12 b:11.9 occ:1.00 O6 A:DG4 2.7 13.6 1.0 O6 A:DG8 2.8 11.7 1.0 O6 A:DG3 2.9 12.3 1.0 O6 A:DG9 2.9 10.9 1.0 K A:K13 3.3 7.8 0.5 C6 A:DG3 3.7 12.3 1.0 C6 A:DG9 3.7 10.2 1.0 C6 A:DG4 3.7 13.1 1.0 C6 A:DG8 3.7 11.0 1.0 N1 A:DG9 3.9 10.0 1.0 N1 A:DG8 4.0 10.9 1.0 N1 A:DG4 4.0 12.6 1.0 N1 A:DG3 4.0 12.3 1.0 C7 A:DT7 4.3 16.9 1.0 C5 A:DG3 4.8 12.5 1.0 C5 A:DG9 4.9 9.8 1.0 C5 A:DT7 5.0 16.3 1.0 C5 A:DG8 5.0 11.0 1.0

Potassium binding site 2 out of 4 in the G4T3G4 Dimeric Quadruplex Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of G4T3G4 Dimeric Quadruplex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K13 b:7.8 occ:0.50 O6 A:DG3 2.7 12.3 1.0 O6 A:DG9 2.8 10.9 1.0 O6 A:DG10 2.9 10.6 1.0 O6 A:DG2 2.9 13.1 1.0 K A:K12 3.3 11.9 1.0 C6 A:DG9 3.6 10.2 1.0 C6 A:DG3 3.7 12.3 1.0 C6 A:DG2 3.7 13.3 1.0 N1 A:DG9 3.8 10.0 1.0 C6 A:DG10 3.8 10.0 1.0 N1 A:DG2 3.9 12.8 1.0 N1 A:DG3 3.9 12.3 1.0 N1 A:DG10 4.1 9.4 1.0 C5 A:DG9 4.9 9.8 1.0 C5 A:DG2 4.9 13.2 1.0 C5 A:DG3 4.9 12.5 1.0

Potassium binding site 3 out of 4 in the G4T3G4 Dimeric Quadruplex Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of G4T3G4 Dimeric Quadruplex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K14 b:36.4 occ:1.00 O A:HOH55 2.8 36.4 0.5 C8 A:DG1 4.1 17.9 1.0 C4' A:DG2 4.2 19.2 1.0 O4' A:DG2 4.2 17.6 1.0 C5' A:DG2 4.3 20.5 1.0 C1' A:DG1 4.4 19.9 1.0 O A:HOH63 4.5 39.8 1.0 N9 A:DG1 4.7 18.9 1.0 O A:HOH61 4.7 34.4 1.0 O A:HOH37 4.8 35.4 1.0

Potassium binding site 4 out of 4 in the G4T3G4 Dimeric Quadruplex Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of G4T3G4 Dimeric Quadruplex Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K15 b:24.2 occ:1.00 N2 A:DG10 3.7 10.0 1.0 O5' A:DG10 3.8 17.6 1.0 C2' A:DG9 4.0 14.7 1.0 C5' A:DG10 4.4 15.3 1.0 N3 A:DG10 4.4 10.1 1.0 C2 A:DG10 4.5 10.2 1.0 OP2 A:DG10 4.7 19.6 1.0 P A:DG10 4.8 19.2 1.0 C3' A:DG9 4.8 15.8 1.0

P.Hazel, G.N.Parkinson, S.Neidle. Topology Variation and Loop Structural Homology in Crystal and Simulated Structures of A Bimolecular Dna Quadruplex. J.Am.Chem.Soc. V. 128 5480 2006.
ISSN: ISSN 0002-7863
PubMed: 16620121
DOI: 10.1021/JA058577+