Sodium in PDB 6pnk: Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX

The structure of Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX, PDB code: 6pnk was solved by L.A.Yatsunyk, L.Y.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.78 / 2.39
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	60.930, 60.930, 194.342, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 24.9

The structure of Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX (pdb code 6pnk). 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 Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX, PDB code: 6pnk:

Sodium binding site 1 out of 1 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:0.6 occ:1.00 O2 B:FMT105 2.7 0.2 1.0 OP1 B:DG18 3.6 0.1 1.0 C B:FMT105 3.7 0.7 1.0 P B:DG18 4.3 0.9 1.0 OP2 B:DG18 4.4 0.2 1.0 O5' B:DG18 4.6 0.5 1.0 O1 B:FMT105 4.6 0.3 1.0

L.Y.Lin, S.Mccarthy, B.M.Powell, Y.Manurung, I.M.Xiang, W.L.Dean, B.Chaires, L.A.Yatsunyk. Biophysical and X-Ray Structural Studies of the (Gggtt)3GGG G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX. Plos One V. 15 41513 2020.
ISSN: ESSN 1932-6203
PubMed: 33206666
DOI: 10.1371/JOURNAL.PONE.0241513