Sodium in PDB 9c46: Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter

The structure of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter, PDB code: 9c46 was solved by E.R.Xing, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.10 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.137, 31.491, 31.5, 90, 104.31, 90
R / Rfree (%)	23.3 / 25.4

The structure of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Sodium atom in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter (pdb code 9c46). 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 Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter, PDB code: 9c46:

Sodium binding site 1 out of 1 in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:83.3 occ:1.00 O4 A:DT2 4.0 90.5 1.0 N3 A:DT2 4.2 78.6 1.0 O2 A:DT11 4.4 81.5 1.0 C4 A:DT2 4.5 78.0 1.0 C5 A:DG12 4.6 60.5 1.0 C4 A:DG12 4.6 60.1 1.0 N7 A:DG12 4.8 62.5 1.0 N9 A:DG12 4.8 65.2 1.0 C6 A:DG12 4.9 59.2 1.0 C8 A:DG12 4.9 65.6 1.0 N3 A:DG12 4.9 58.6 1.0

P.Seth, E.Xing, A.D.Hendrickson, K.Li, R.Monsen, J.B.Chaires, S.Neidle, L.A.Yatsunyk. Interaction of N-Methylmesoporphyrin IX with A Hybrid Left-/Right-Handed G-Quadruplex Motif From the Promoter of the SLC2A1 Gene. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39704129
DOI: 10.1093/NAR/GKAE1208