Potassium in PDB 7d5d: Left-Handed G-Quadruplex Containing One Bulge

The structure of Left-Handed G-Quadruplex Containing One Bulge, PDB code: 7d5d was solved by P.Das, K.H.Ngo, F.R.Winnerdy, A.Maity, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.33 / 1.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.215, 40.037, 30.376, 90, 115.87, 90
R / Rfree (%)	11.9 / 16.8

The binding sites of Potassium atom in the Left-Handed G-Quadruplex Containing One Bulge (pdb code 7d5d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Left-Handed G-Quadruplex Containing One Bulge, PDB code: 7d5d:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Left-Handed G-Quadruplex Containing One Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Left-Handed G-Quadruplex Containing One Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:6.2 occ:1.00 O6 A:DG22 2.7 7.0 1.0 O6 A:DG19 2.8 7.2 1.0 O6 A:DG25 2.8 6.8 1.0 O6 A:DG14 2.8 6.2 1.0 O6 A:DG17 2.8 5.8 1.0 O6 A:DG16 2.8 7.8 1.0 O6 A:DG23 2.9 5.9 1.0 O6 A:DG20 2.9 6.1 1.0 K A:K104 3.6 6.1 1.0 N14 A:SPM102 3.6 11.7 0.5 C6 A:DG22 3.6 5.4 1.0 C6 A:DG19 3.6 6.8 1.0 C6 A:DG16 3.6 7.3 1.0 C6 A:DG14 3.7 5.3 1.0 C6 A:DG25 3.7 6.2 1.0 C6 A:DG17 3.7 6.0 1.0 C6 A:DG23 3.8 5.5 1.0 N1 A:DG22 3.8 6.0 1.0 C6 A:DG20 3.8 5.7 1.0 N1 A:DG19 3.8 6.0 1.0 N1 A:DG16 3.9 7.0 1.0 N1 A:DG14 4.0 5.6 1.0 N1 A:DG25 4.0 6.0 1.0 N1 A:DG17 4.1 6.4 1.0 N1 A:DG23 4.1 5.1 1.0 N1 A:DG20 4.2 5.6 1.0 C13 A:SPM102 4.8 18.7 0.5 C5 A:DG22 4.8 6.7 1.0 C5 A:DG14 4.8 5.4 1.0 C5 A:DG19 4.8 6.3 1.0 C5 A:DG16 4.9 7.3 1.0 C5 A:DG17 4.9 6.5 1.0 C13 A:SPM102 4.9 27.6 0.5 C5 A:DG25 5.0 7.1 1.0

Potassium binding site 2 out of 3 in the Left-Handed G-Quadruplex Containing One Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Left-Handed G-Quadruplex Containing One Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:6.1 occ:1.00 O6 A:DG14 2.8 6.2 1.0 O6 A:DG20 2.8 6.1 1.0 O6 A:DG9 2.8 6.1 1.0 O6 A:DG23 2.8 5.9 1.0 O6 A:DG2 2.8 6.0 1.0 O6 A:DG6 2.8 6.4 1.0 O6 A:DG12 2.8 5.9 1.0 O6 A:DG17 2.9 5.8 1.0 K A:K105 3.5 6.0 1.0 K A:K103 3.6 6.2 1.0 C6 A:DG20 3.6 5.7 1.0 C6 A:DG9 3.6 5.5 1.0 C6 A:DG23 3.7 5.5 1.0 C6 A:DG14 3.7 5.3 1.0 C6 A:DG6 3.7 5.7 1.0 C6 A:DG2 3.7 5.8 1.0 C6 A:DG12 3.7 5.6 1.0 C6 A:DG17 3.8 6.0 1.0 N1 A:DG20 3.9 5.6 1.0 N1 A:DG23 4.0 5.1 1.0 N1 A:DG9 4.0 5.8 1.0 N1 A:DG6 4.0 5.2 1.0 N1 A:DG14 4.0 5.6 1.0 N1 A:DG2 4.1 5.4 1.0 N1 A:DG12 4.1 5.9 1.0 N1 A:DG17 4.1 6.4 1.0 C5 A:DG23 4.8 6.4 1.0 C5 A:DG20 4.8 6.2 1.0 C5 A:DG9 4.8 5.7 1.0 C5 A:DG14 4.9 5.4 1.0 C5 A:DG6 4.9 5.7 1.0 C5 A:DG2 4.9 6.2 1.0 C5 A:DG12 4.9 5.6 1.0 C5 A:DG17 5.0 6.5 1.0

Potassium binding site 3 out of 3 in the Left-Handed G-Quadruplex Containing One Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Left-Handed G-Quadruplex Containing One Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:6.0 occ:1.00 O6 A:DG4 2.7 6.8 1.0 O6 A:DG8 2.7 7.8 1.0 O6 A:DG11 2.7 6.2 1.0 O6 A:DG1 2.8 7.4 1.0 O6 A:DG2 2.8 6.0 1.0 O6 A:DG12 2.9 5.9 1.0 O6 A:DG9 2.9 6.1 1.0 O6 A:DG6 2.9 6.4 1.0 K A:K104 3.5 6.1 1.0 C6 A:DG8 3.6 6.5 1.0 C6 A:DG4 3.6 6.1 1.0 C6 A:DG1 3.6 6.1 1.0 C6 A:DG11 3.6 6.0 1.0 C6 A:DG2 3.7 5.8 1.0 C6 A:DG12 3.7 5.6 1.0 C6 A:DG9 3.8 5.5 1.0 N1 A:DG8 3.8 6.5 1.0 C6 A:DG6 3.8 5.7 1.0 N1 A:DG1 3.9 6.4 1.0 N1 A:DG4 3.9 6.8 1.0 N1 A:DG11 3.9 6.7 1.0 N1 A:DG12 4.0 5.9 1.0 N1 A:DG2 4.0 5.4 1.0 N1 A:DG9 4.1 5.8 1.0 N1 A:DG6 4.2 5.2 1.0 C5 A:DG8 4.8 6.4 1.0 C5 A:DG11 4.9 6.2 1.0 C5 A:DG2 4.9 6.2 1.0 C5 A:DG12 4.9 5.6 1.0 C5 A:DG1 4.9 7.3 1.0 C5 A:DG4 4.9 6.8 1.0 C5 A:DG9 5.0 5.7 1.0

P.Das, K.H.Ngo, F.R.Winnerdy, A.Maity, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan. Bulges in Left-Handed G-Quadruplexes. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33503265
DOI: 10.1093/NAR/GKAA1259