Sodium in PDB 8vjt: Structure of the Poly-Ug Quadruplex (Gugugu)4

The structure of Structure of the Poly-Ug Quadruplex (Gugugu)4, PDB code: 8vjt was solved by C.A.Bingman, E.J.Montemayor, S.Roschdi, Y.Nomura, S.E.Butcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.73 / 1.05
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	32.821, 32.821, 57.97, 90, 90, 90
R / Rfree (%)	14.8 / 16.1

The structure of Structure of the Poly-Ug Quadruplex (Gugugu)4 also contains other interesting chemical elements:

Potassium

(K)

7 atoms

The binding sites of Sodium atom in the Structure of the Poly-Ug Quadruplex (Gugugu)4 (pdb code 8vjt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Poly-Ug Quadruplex (Gugugu)4, PDB code: 8vjt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:11.1 occ:1.00 O3' A:U6 2.3 9.8 0.5 O A:HOH206 2.4 11.3 1.0 O A:HOH220 2.5 14.9 0.5 O A:HOH204 2.5 10.3 1.0 O2' A:U6 2.5 10.2 0.5 O3' A:U6 2.6 12.8 0.5 O2' A:U6 2.6 10.1 0.5 H1' A:U6 3.3 11.3 0.5 C2' A:U6 3.3 9.5 0.5 C3' A:U6 3.3 9.2 0.5 C2' A:U6 3.5 10.3 0.5 C3' A:U6 3.5 12.7 0.5 H1' A:U6 3.6 12.9 0.5 C1' A:U6 3.8 9.4 0.5 H3' A:U6 3.8 11.0 0.5 OP2 A:G5 3.8 15.4 0.5 OP2 A:G5 3.9 8.4 0.5 H3' A:U6 3.9 15.3 0.5 C1' A:U6 4.1 10.8 0.5 H2' A:U6 4.2 11.4 0.5 OP1 A:U4 4.2 16.3 0.5 O A:HOH216 4.2 35.4 1.0 H2' A:U6 4.3 12.3 0.5 O A:HOH223 4.3 21.2 1.0 O2 A:U6 4.4 9.7 0.5 OP2 A:U4 4.5 16.6 0.5 C4' A:U6 4.5 9.3 0.5 OP2 A:U4 4.5 9.5 0.5 H4' A:U6 4.6 11.1 0.5 OP1 A:U4 4.6 9.3 0.5 O4' A:U6 4.7 10.7 0.5 O2 A:U6 4.7 9.1 0.5 P A:U4 4.7 16.6 0.5 C4' A:U6 4.8 12.0 0.5 N1 A:U6 4.8 8.4 0.5 H4' A:U6 4.9 14.4 0.5 C2 A:U6 5.0 8.5 0.5

Sodium binding site 2 out of 2 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:22.6 occ:1.00 O B:HOH206 2.1 21.0 1.0 O B:HOH210 2.2 28.1 1.0 O B:HOH203 2.4 15.9 0.5 O2' B:U6 2.4 13.6 0.5 O B:HOH203 2.4 14.5 0.5 O2' B:U6 2.5 12.5 0.5 O3' B:U6 2.5 17.7 0.5 HO3' B:U6 3.0 16.1 0.5 H1' B:U6 3.3 15.2 0.5 C2' B:U6 3.3 13.9 0.5 OP2 B:G5 3.4 12.6 0.5 C3' B:U6 3.4 15.9 0.5 O3' B:U6 3.8 13.4 0.5 C2' B:U6 3.8 10.9 0.5 OP2 B:G5 3.8 10.1 0.5 C1' B:U6 3.8 12.6 0.5 H3' B:U6 3.9 19.0 0.5 H1' B:U6 4.1 12.3 0.5 H2' B:U6 4.1 16.7 0.5 O2 B:U6 4.2 9.4 0.5 C3' B:U6 4.4 12.1 0.5 H2' B:U6 4.4 13.1 0.5 C1' B:U6 4.5 10.2 0.5 O2 B:U6 4.5 9.0 0.5 OP2 B:U4 4.6 19.2 0.5 C4' B:U6 4.6 15.2 0.5 P B:G5 4.7 12.3 0.5 H5' B:U4 4.7 14.7 0.5 H3' B:U6 4.7 14.5 0.5 H4' B:U6 4.8 18.3 0.5 O4' B:U6 4.8 14.3 0.5 N1 B:U6 4.8 9.8 0.5 C2 B:U6 4.9 8.4 0.5 O B:HOH201 4.9 16.4 0.5 OP1 B:G5 5.0 12.4 0.5

S.Roschdi, E.J.Montemayor, R.Vivek, C.A.Bingman, S.E.Butcher. Self-Assembly and Condensation of Intermolecular Poly(Ug) Rna Quadruplexes. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39373474
DOI: 10.1093/NAR/GKAE870