Sodium in PDB 7d5e: Left-Handed G-Quadruplex Containing Two Bulges

The structure of Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e was solved by P.Das, A.Maity, K.H.Ngo, F.R.Winnerdy, 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)	29.09 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.1, 39.81, 54.97, 90, 91.28, 90
R / Rfree (%)	18.4 / 21.4

The structure of Left-Handed G-Quadruplex Containing Two Bulges also contains other interesting chemical elements:

Potassium

(K)

7 atoms

The binding sites of Sodium atom in the Left-Handed G-Quadruplex Containing Two Bulges (pdb code 7d5e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e:

Sodium binding site 1 out of 1 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:12.9 occ:1.00 O B:HOH207 2.7 19.5 1.0 O4' B:DT9 2.7 14.3 1.0 O B:HOH235 2.9 23.3 1.0 O2 B:DT9 3.1 15.1 1.0 O5' B:DT9 3.1 16.0 1.0 C1' B:DT9 3.7 14.6 1.0 C2 B:DT9 3.7 14.4 1.0 C4' B:DT9 3.8 14.7 1.0 C5' B:DT9 3.9 15.5 1.0 N1 B:DT9 4.0 14.0 1.0 OP2 B:DT9 4.1 17.1 1.0 P B:DT9 4.3 15.2 1.0 O B:HOH301 4.4 22.3 1.0 C7 B:DT11 4.5 15.4 1.0 N3 B:DT9 4.7 14.4 1.0 OP2 B:DT11 4.8 16.0 1.0 O B:HOH298 4.9 37.2 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