Potassium 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:

Sodium

(Na)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the Structure of the Poly-Ug Quadruplex (Gugugu)4, PDB code: 8vjt:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K101 b:7.3 occ:0.25 O6 A:G1 2.7 8.1 0.5 O6 B:G1 2.8 8.0 0.5 O6 B:G1 2.8 6.7 0.5 O6 A:G1 2.9 7.9 0.5 H1 B:G1 3.4 9.8 0.5 K B:K103 3.5 7.4 0.2 K A:K102 3.5 8.1 0.2 H1 A:G1 3.5 8.6 0.5 C6 A:G1 3.6 6.7 0.5 C6 B:G1 3.7 8.1 0.5 H1 A:G1 3.7 11.9 0.5 H1 B:G1 3.7 8.6 0.5 C6 B:G1 3.7 6.7 0.5 C6 A:G1 3.8 9.5 0.5 N1 B:G1 3.8 8.1 0.5 N1 A:G1 3.9 7.2 0.5 N1 A:G1 4.1 9.9 0.5 N1 B:G1 4.1 7.1 0.5 C5 A:G1 4.8 5.5 0.5 C5 B:G1 4.9 6.9 0.5 C5 B:G1 4.9 8.8 0.5 C5 A:G1 4.9 12.0 0.5

Potassium binding site 2 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:8.1 occ:0.25 O6 A:G3 2.7 9.2 0.5 O6 A:G1 2.8 7.9 0.5 O6 A:G3 2.8 7.2 0.5 O6 A:G1 2.9 8.1 0.5 O A:HOH210 3.3 4.5 0.2 H1 A:G3 3.5 8.6 0.5 K A:K101 3.5 7.3 0.2 C6 A:G3 3.6 7.2 0.5 H1 A:G1 3.6 8.6 0.5 H1 A:G3 3.6 9.1 0.5 C6 A:G3 3.7 7.5 0.5 C6 A:G1 3.7 6.7 0.5 H1 A:G1 3.7 11.9 0.5 C6 A:G1 3.7 9.5 0.5 N1 A:G3 3.9 7.2 0.5 N1 A:G1 4.0 7.2 0.5 N1 A:G3 4.0 7.6 0.5 N1 A:G1 4.1 9.9 0.5 C5 A:G3 4.7 6.9 0.5 C5 A:G3 4.9 9.1 0.5 C5 A:G1 4.9 5.5 0.5 C5 A:G1 4.9 12.0 0.5

Potassium binding site 3 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:8.6 occ:0.25 O4 A:U4 2.7 6.1 0.5 O4 A:U4 2.7 12.9 0.5 O6 A:G5 2.7 5.4 0.5 O6 A:G5 2.8 9.7 0.5 O A:HOH210 3.0 4.5 0.2 H3 A:U4 3.4 6.8 0.5 K A:K104 3.4 8.8 0.2 H1 A:G5 3.5 10.6 0.5 H3 A:U4 3.6 15.2 0.5 C4 A:U4 3.6 6.6 0.5 H1 A:G5 3.7 8.7 0.5 C4 A:U4 3.7 11.2 0.5 C6 A:G5 3.7 6.0 0.5 C6 A:G5 3.8 9.2 0.5 N3 A:U4 3.8 5.7 0.5 N1 A:G5 4.0 8.8 0.5 N3 A:U4 4.0 12.7 0.5 N1 A:G5 4.1 7.2 0.5 C5 A:U4 4.9 7.6 0.5 C5 A:G5 5.0 6.5 0.5

Potassium binding site 4 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:8.8 occ:0.25 O4 A:U6 2.7 9.9 0.5 O4 A:U6 2.8 7.6 0.5 O6 A:G5 2.9 5.4 0.5 O6 A:G5 3.0 9.7 0.5 H3 A:U6 3.3 10.2 0.5 K A:K103 3.4 8.6 0.2 H3 A:U6 3.5 10.0 0.5 H1 A:G5 3.5 10.6 0.5 C6 A:G5 3.6 6.0 0.5 C4 A:U6 3.6 9.8 0.5 H1 A:G5 3.6 8.7 0.5 C6 A:G5 3.7 9.2 0.5 C4 A:U6 3.8 7.4 0.5 N3 A:U6 3.8 8.5 0.5 N1 A:G5 3.9 8.8 0.5 N1 A:G5 3.9 7.2 0.5 N3 A:U6 4.0 8.4 0.5 C5 A:G5 4.8 6.5 0.5 C5 A:G5 4.8 10.2 0.5 C5 A:U6 4.9 10.2 0.5

Potassium binding site 5 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:6.3 occ:0.25 O4 B:U6 2.7 7.6 0.5 O6 B:G5 2.8 5.8 0.5 O4 B:U6 2.8 7.8 0.5 O6 B:G5 2.9 7.5 0.5 H3 B:U6 3.4 8.5 0.5 H3 B:U6 3.4 10.0 0.5 H1 B:G5 3.5 8.1 0.5 K B:K102 3.5 6.2 0.2 C6 B:G5 3.6 6.9 0.5 H1 B:G5 3.6 8.6 0.5 C6 B:G5 3.6 7.5 0.5 C4 B:U6 3.7 7.8 0.5 C4 B:U6 3.7 7.6 0.5 N1 B:G5 3.9 6.7 0.5 N1 B:G5 3.9 7.1 0.5 N3 B:U6 3.9 8.3 0.5 N3 B:U6 4.0 7.1 0.5 C5 B:G5 4.7 7.9 0.5 C5 B:G5 4.8 7.0 0.5

Potassium binding site 6 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:6.2 occ:0.25 O4 B:U4 2.7 6.4 0.5 O4 B:U4 2.7 9.3 0.5 O6 B:G5 2.8 5.8 0.5 O6 B:G5 2.9 7.5 0.5 H3 B:U4 3.3 11.8 0.5 H3 B:U4 3.4 7.6 0.5 K B:K101 3.5 6.3 0.2 C4 B:U4 3.6 6.3 0.5 C4 B:U4 3.7 9.6 0.5 H1 B:G5 3.7 8.1 0.5 C6 B:G5 3.8 6.9 0.5 H1 B:G5 3.8 8.6 0.5 N3 B:U4 3.8 9.8 0.5 C6 B:G5 3.9 7.5 0.5 N3 B:U4 3.9 6.3 0.5 N1 B:G5 4.1 6.7 0.5 N1 B:G5 4.2 7.1 0.5 C5 B:U4 4.9 6.8 0.5 C5 B:U4 5.0 9.9 0.5 C5 B:G5 5.0 7.9 0.5

Potassium binding site 7 out of 7 in the Structure of the Poly-Ug Quadruplex (Gugugu)4


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of the Poly-Ug Quadruplex (Gugugu)4 within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:7.4 occ:0.25 O6 B:G3 2.6 13.0 0.5 O6 B:G3 2.6 4.0 0.5 O6 B:G1 2.9 6.7 0.5 O6 B:G1 3.0 8.0 0.5 H1 B:G3 3.3 12.9 0.5 H1 B:G3 3.5 5.3 0.5 K A:K101 3.5 7.3 0.2 H1 B:G1 3.5 9.8 0.5 C6 B:G3 3.6 4.5 0.5 C6 B:G3 3.6 10.8 0.5 C6 B:G1 3.7 8.1 0.5 H1 B:G1 3.8 8.6 0.5 C6 B:G1 3.8 6.7 0.5 N1 B:G3 3.8 10.8 0.5 N1 B:G3 3.9 4.4 0.5 N1 B:G1 3.9 8.1 0.5 N1 B:G1 4.1 7.1 0.5 C5 B:G3 4.8 6.8 0.5 C5 B:G3 4.9 8.6 0.5 C5 B:G1 4.9 8.8 0.5 C5 B:G1 5.0 6.9 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