Potassium in PDB 6n65: Kras G-Quadruplex G16T Mutant.

The structure of Kras G-Quadruplex G16T Mutant., PDB code: 6n65 was solved by J.W.Schmidberger, A.Ou, N.M.Smith, K.S.Iyer, C.S.Bond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.41 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.693, 30.127, 52.970, 90.00, 94.51, 90.00
R / Rfree (%)	21 / 24.1

The binding sites of Potassium atom in the Kras G-Quadruplex G16T Mutant. (pdb code 6n65). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Kras G-Quadruplex G16T Mutant., PDB code: 6n65:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Kras G-Quadruplex G16T Mutant.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Kras G-Quadruplex G16T Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:14.6 occ:1.00 O6 A:DG2 2.7 16.7 0.4 O6 B:DG2 2.8 16.0 0.4 O6 A:DG11 2.8 17.0 1.0 O6 B:DG18 2.8 16.1 1.0 O6 B:DG6 2.8 15.3 1.0 O6 A:DG18 2.8 16.3 1.0 O6 A:DG2 2.8 17.0 0.6 O6 B:DG11 2.8 17.3 1.0 O6 B:DG2 2.8 16.0 0.6 O6 A:DG6 2.8 15.0 1.0 K B:K101 3.4 15.6 1.0 K A:K102 3.4 15.6 1.0 C6 A:DG11 3.7 15.5 1.0 C6 B:DG18 3.7 15.0 1.0 C6 A:DG2 3.7 15.1 0.4 C6 B:DG11 3.7 16.2 1.0 C6 A:DG18 3.7 14.8 1.0 C6 A:DG2 3.7 14.9 0.6 C6 B:DG2 3.7 13.9 0.6 C6 B:DG2 3.7 14.0 0.4 C6 B:DG6 3.7 18.0 1.0 C6 A:DG6 3.7 16.5 1.0 N1 B:DG11 3.9 13.6 1.0 N1 A:DG11 3.9 13.9 1.0 N1 B:DG2 3.9 14.4 0.6 N1 B:DG18 3.9 16.0 1.0 N1 A:DG2 4.0 15.4 0.6 N1 A:DG18 4.0 16.5 1.0 N1 A:DG2 4.0 15.5 0.4 N1 B:DG6 4.0 15.0 1.0 N1 A:DG6 4.0 14.4 1.0 N1 B:DG2 4.1 15.6 0.4 C5 B:DG2 4.9 16.6 0.4 C5 A:DG2 4.9 16.1 0.4 C5 A:DG18 4.9 14.4 1.0 C5 B:DG18 4.9 13.5 1.0 C5 A:DG11 4.9 16.1 1.0 C5 B:DG11 4.9 15.5 1.0 C5 A:DG2 4.9 15.7 0.6 C5 B:DG2 4.9 17.0 0.6 C5 A:DG6 4.9 16.6 1.0 C5 B:DG6 4.9 18.0 1.0

Potassium binding site 2 out of 5 in the Kras G-Quadruplex G16T Mutant.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Kras G-Quadruplex G16T Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:15.6 occ:1.00 O6 A:DG12 2.6 16.0 1.0 O6 A:DG7 2.7 16.8 1.0 O6 A:DG2 2.7 17.0 0.6 O6 A:DG19 2.7 16.8 1.0 O6 A:DG3 2.8 17.4 1.0 O6 A:DG6 2.8 15.0 1.0 O6 A:DG18 2.8 16.3 1.0 O6 A:DG2 2.8 16.7 0.4 O6 A:DG11 2.9 17.0 1.0 K A:K101 3.4 14.6 1.0 K A:K103 3.4 16.1 1.0 C6 A:DG2 3.6 14.9 0.6 C6 A:DG12 3.6 15.6 1.0 C6 A:DG19 3.6 17.7 1.0 C6 A:DG3 3.7 17.2 1.0 C6 A:DG7 3.7 17.2 1.0 C6 A:DG2 3.7 15.1 0.4 C6 A:DG6 3.7 16.5 1.0 C6 A:DG18 3.7 14.8 1.0 C6 A:DG11 3.7 15.5 1.0 N1 A:DG2 3.9 15.4 0.6 N1 A:DG12 3.9 17.1 1.0 N1 A:DG19 3.9 18.3 1.0 N1 A:DG2 4.0 15.5 0.4 N1 A:DG3 4.0 16.1 1.0 N1 A:DG6 4.0 14.4 1.0 N1 A:DG7 4.0 19.7 1.0 N1 A:DG18 4.0 16.5 1.0 N1 A:DG11 4.0 13.9 1.0 C5 A:DG2 4.8 15.7 0.6 C5 A:DG19 4.9 15.9 1.0 C5 A:DG6 4.9 16.6 1.0 C5 A:DG2 4.9 16.1 0.4 C5 A:DG12 4.9 17.3 1.0 C5 A:DG3 4.9 18.8 1.0 C5 A:DG7 4.9 16.1 1.0 C5 A:DG18 4.9 14.4 1.0 C5 A:DG11 4.9 16.1 1.0

Potassium binding site 3 out of 5 in the Kras G-Quadruplex G16T Mutant.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Kras G-Quadruplex G16T Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:16.1 occ:1.00 O6 A:DG4 2.6 19.2 1.0 O6 A:DG20 2.7 17.9 1.0 O6 A:DG13 2.7 15.9 1.0 O6 A:DG9 2.7 17.4 1.0 O6 A:DG19 2.9 16.8 1.0 O6 A:DG7 2.9 16.8 1.0 O6 A:DG12 3.0 16.0 1.0 O6 A:DG3 3.0 17.4 1.0 K A:K102 3.4 15.6 1.0 C6 A:DG4 3.6 17.0 1.0 C6 A:DG20 3.7 19.6 1.0 C6 A:DG9 3.7 17.7 1.0 C6 A:DG12 3.7 15.6 1.0 C6 A:DG13 3.7 17.8 1.0 C6 A:DG7 3.7 17.2 1.0 C6 A:DG19 3.8 17.7 1.0 C6 A:DG3 3.8 17.2 1.0 N1 A:DG4 3.8 16.1 1.0 N1 A:DG9 3.9 21.3 1.0 N1 A:DG20 3.9 19.1 1.0 N1 A:DG13 4.0 18.8 1.0 N1 A:DG12 4.0 17.1 1.0 N1 A:DG7 4.0 19.7 1.0 N1 A:DG19 4.1 18.3 1.0 N1 A:DG3 4.1 16.1 1.0 N6 A:DA22 4.3 20.6 1.0 C6 A:DA22 4.8 20.4 1.0 C5 A:DG12 4.8 17.3 1.0 C5 A:DG7 4.9 16.1 1.0 C5 A:DG4 4.9 17.4 1.0 C5 A:DG9 4.9 16.5 1.0 C5 A:DG19 5.0 15.9 1.0 C5 A:DG20 5.0 18.6 1.0 C5 A:DG3 5.0 18.8 1.0

Potassium binding site 4 out of 5 in the Kras G-Quadruplex G16T Mutant.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Kras G-Quadruplex G16T Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:15.6 occ:1.00 O6 B:DG12 2.7 16.4 1.0 O6 B:DG2 2.7 16.0 0.4 O6 B:DG7 2.7 15.6 1.0 O6 B:DG19 2.7 16.0 1.0 O6 B:DG3 2.8 18.4 1.0 O6 B:DG6 2.8 15.3 1.0 O6 B:DG2 2.8 16.0 0.6 O6 B:DG18 2.9 16.1 1.0 O6 B:DG11 2.9 17.3 1.0 K A:K101 3.4 14.6 1.0 K B:K102 3.4 16.2 1.0 C6 B:DG19 3.6 16.7 1.0 C6 B:DG12 3.6 17.0 1.0 C6 B:DG2 3.6 14.0 0.4 C6 B:DG2 3.6 13.9 0.6 C6 B:DG6 3.7 18.0 1.0 C6 B:DG3 3.7 19.2 1.0 C6 B:DG7 3.7 17.6 1.0 C6 B:DG18 3.7 15.0 1.0 C6 B:DG11 3.7 16.2 1.0 N1 B:DG2 3.9 14.4 0.6 N1 B:DG19 3.9 18.5 1.0 N1 B:DG12 3.9 17.4 1.0 N1 B:DG3 4.0 16.0 1.0 N1 B:DG11 4.0 13.6 1.0 N1 B:DG18 4.0 16.0 1.0 N1 B:DG6 4.0 15.0 1.0 N1 B:DG7 4.0 18.7 1.0 N1 B:DG2 4.1 15.6 0.4 C5 B:DG2 4.8 16.6 0.4 C5 B:DG19 4.8 16.8 1.0 C5 B:DG6 4.9 18.0 1.0 C5 B:DG2 4.9 17.0 0.6 C5 B:DG12 4.9 15.3 1.0 C5 B:DG3 4.9 18.2 1.0 C5 B:DG18 4.9 13.5 1.0 C5 B:DG7 4.9 17.7 1.0 C5 B:DG11 4.9 15.5 1.0

Potassium binding site 5 out of 5 in the Kras G-Quadruplex G16T Mutant.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Kras G-Quadruplex G16T Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:16.2 occ:1.00 O6 B:DG4 2.7 18.8 1.0 O6 B:DG20 2.7 16.6 1.0 O6 B:DG13 2.7 15.8 1.0 O6 B:DG9 2.8 16.3 1.0 O6 B:DG19 2.9 16.0 1.0 O6 B:DG3 3.0 18.4 1.0 O6 B:DG7 3.0 15.6 1.0 O6 B:DG12 3.0 16.4 1.0 K B:K101 3.4 15.6 1.0 C6 B:DG4 3.6 17.9 1.0 C6 B:DG20 3.6 18.9 1.0 C6 B:DG9 3.7 19.4 1.0 C6 B:DG13 3.7 16.8 1.0 C6 B:DG12 3.7 17.0 1.0 C6 B:DG19 3.7 16.7 1.0 C6 B:DG7 3.8 17.6 1.0 C6 B:DG3 3.8 19.2 1.0 N1 B:DG9 3.9 20.1 1.0 N1 B:DG4 3.9 15.6 1.0 N1 B:DG20 3.9 18.5 1.0 N1 B:DG13 3.9 18.7 1.0 N1 B:DG12 4.0 17.4 1.0 N1 B:DG19 4.1 18.5 1.0 N1 B:DG7 4.1 18.7 1.0 N1 B:DG3 4.1 16.0 1.0 N6 B:DA22 4.3 19.7 1.0 C6 B:DA22 4.8 19.9 1.0 C5 B:DG12 4.9 15.3 1.0 C5 B:DG7 4.9 17.7 1.0 C5 B:DG4 4.9 17.6 1.0 C5 B:DG20 4.9 18.2 1.0 C5 B:DG19 4.9 16.8 1.0 C5 B:DG9 5.0 15.4 1.0 C5 B:DG13 5.0 19.0 1.0

A.Ou, N.M.Smith. High Resolution Crystal Structure of A Kras Promoter G-Quadruplex Reveals A Dimer with Extensive Poly-A Pi-Stacking Interactions For Small-Molecule Recognition Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAA262