Potassium in PDB 6wck: Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.

The structure of Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16., PDB code: 6wck 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)	33.34 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.452, 29.943, 52.691, 90.00, 94.62, 90.00
R / Rfree (%)	19.7 / 24.1

The structure of Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16. also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Potassium atom in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16. (pdb code 6wck). 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 with Bromo Uracil Replacing T8 and T16., PDB code: 6wck:
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 with Bromo Uracil Replacing T8 and T16.


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 with Bromo Uracil Replacing T8 and T16. within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:11.8 occ:1.00 O6 A:DG2 2.6 13.8 0.5 O6 B:DG2 2.7 15.4 0.4 O6 A:DG18 2.7 12.6 1.0 O6 A:DG11 2.7 14.1 1.0 O6 B:DG18 2.8 15.0 1.0 O6 B:DG11 2.8 15.8 1.0 O6 A:DG6 2.8 15.6 1.0 O6 B:DG2 2.8 15.9 0.6 O6 A:DG2 2.9 12.4 0.5 O6 B:DG6 2.9 12.8 1.0 K A:K102 3.3 13.4 1.0 K B:K101 3.3 12.0 1.0 C6 A:DG18 3.6 12.9 1.0 C6 B:DG18 3.6 12.7 1.0 C6 A:DG11 3.6 15.8 1.0 C6 B:DG2 3.6 13.4 0.4 C6 A:DG2 3.6 13.1 0.5 C6 B:DG11 3.6 13.6 1.0 C6 B:DG2 3.7 14.0 0.6 C6 A:DG2 3.7 13.8 0.5 C6 A:DG6 3.7 14.7 1.0 C6 B:DG6 3.7 15.9 1.0 N1 B:DG18 3.9 14.1 1.0 N1 B:DG11 3.9 14.3 1.0 N1 A:DG11 3.9 11.7 1.0 N1 B:DG2 3.9 11.8 0.6 N1 A:DG18 4.0 12.3 1.0 N1 A:DG2 4.0 10.7 0.5 N1 A:DG2 4.1 11.5 0.5 N1 A:DG6 4.1 16.0 1.0 N1 B:DG6 4.1 13.3 1.0 N1 B:DG2 4.1 12.8 0.4 C5 B:DG2 4.8 12.3 0.4 C5 A:DG2 4.8 12.6 0.5 C5 A:DG18 4.8 9.0 1.0 C5 B:DG18 4.8 11.1 1.0 C5 A:DG11 4.9 10.0 1.0 C5 B:DG11 4.9 12.7 1.0 C5 B:DG2 4.9 12.1 0.6 C5 A:DG2 4.9 12.7 0.5 C5 A:DG6 4.9 13.3 1.0 C5 B:DG6 5.0 18.0 1.0

Potassium binding site 2 out of 5 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


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 with Bromo Uracil Replacing T8 and T16. within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:13.4 occ:1.00 O6 A:DG12 2.6 11.0 1.0 O6 A:DG7 2.7 14.7 1.0 O6 A:DG19 2.7 14.3 1.0 O6 A:DG2 2.8 13.8 0.5 O6 A:DG2 2.8 12.4 0.5 O6 A:DG6 2.8 15.6 1.0 O6 A:DG3 2.8 13.1 1.0 O6 A:DG18 2.8 12.6 1.0 O6 A:DG11 2.8 14.1 1.0 K A:K101 3.3 11.8 1.0 K A:K103 3.4 13.6 1.0 C6 A:DG12 3.6 12.6 1.0 C6 A:DG2 3.6 13.8 0.5 C6 A:DG19 3.6 17.8 1.0 C6 A:DG7 3.6 15.4 1.0 C6 A:DG6 3.7 14.7 1.0 C6 A:DG2 3.7 13.1 0.5 C6 A:DG3 3.7 18.9 1.0 C6 A:DG11 3.7 15.8 1.0 C6 A:DG18 3.7 12.9 1.0 N1 A:DG2 3.8 10.7 0.5 N1 A:DG12 3.9 12.6 1.0 N1 A:DG19 3.9 15.9 1.0 N1 A:DG3 4.0 14.5 1.0 N1 A:DG6 4.0 16.0 1.0 N1 A:DG11 4.0 11.7 1.0 N1 A:DG7 4.0 15.4 1.0 N1 A:DG18 4.1 12.3 1.0 N1 A:DG2 4.1 11.5 0.5 C5 A:DG2 4.8 12.6 0.5 C5 A:DG12 4.8 14.2 1.0 C5 A:DG19 4.8 10.0 1.0 C5 A:DG2 4.9 12.7 0.5 C5 A:DG18 4.9 9.0 1.0 C5 A:DG6 4.9 13.3 1.0 C5 A:DG11 4.9 10.0 1.0 C5 A:DG7 4.9 12.8 1.0 C5 A:DG3 4.9 15.9 1.0

Potassium binding site 3 out of 5 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


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 with Bromo Uracil Replacing T8 and T16. within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:13.6 occ:1.00 O6 A:DG20 2.7 13.3 1.0 O6 A:DG4 2.7 12.6 1.0 O6 A:DG13 2.8 14.7 1.0 O6 A:DG9 2.8 16.4 1.0 O6 A:DG12 2.8 11.0 1.0 O6 A:DG19 2.8 14.3 1.0 O6 A:DG3 2.9 13.1 1.0 O6 A:DG7 2.9 14.7 1.0 K A:K102 3.4 13.4 1.0 C6 A:DG12 3.6 12.6 1.0 C6 A:DG20 3.6 16.0 1.0 C6 A:DG4 3.7 13.8 1.0 C6 A:DG19 3.7 17.8 1.0 C6 A:DG9 3.7 18.1 1.0 C6 A:DG13 3.7 19.8 1.0 C6 A:DG7 3.7 15.4 1.0 C6 A:DG3 3.8 18.9 1.0 N1 A:DG4 3.9 20.3 1.0 N1 A:DG9 3.9 17.9 1.0 N1 A:DG12 3.9 12.6 1.0 N1 A:DG20 3.9 15.8 1.0 N1 A:DG13 4.0 17.5 1.0 N1 A:DG19 4.0 15.9 1.0 N1 A:DG7 4.1 15.4 1.0 N1 A:DG3 4.1 14.5 1.0 N6 A:DA22 4.4 21.8 1.0 C5 A:DG12 4.7 14.2 1.0 C5 A:DG7 4.9 12.8 1.0 C5 A:DG19 4.9 10.0 1.0 C6 A:DA22 4.9 25.2 1.0 C5 A:DG20 4.9 11.4 1.0 C5 A:DG4 4.9 12.6 1.0 C5 A:DG3 5.0 15.9 1.0 C5 A:DG9 5.0 15.4 1.0

Potassium binding site 4 out of 5 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


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 with Bromo Uracil Replacing T8 and T16. within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:12.0 occ:1.00 O6 B:DG2 2.7 15.9 0.6 O6 B:DG12 2.7 14.2 1.0 O6 B:DG7 2.7 12.1 1.0 O6 B:DG19 2.7 13.1 1.0 O6 B:DG2 2.7 15.4 0.4 O6 B:DG3 2.7 16.7 1.0 O6 B:DG18 2.8 15.0 1.0 O6 B:DG6 2.8 12.8 1.0 O6 B:DG11 2.8 15.8 1.0 K A:K101 3.3 11.8 1.0 K B:K102 3.4 12.5 1.0 C6 B:DG2 3.5 14.0 0.6 C6 B:DG19 3.6 14.2 1.0 C6 B:DG2 3.6 13.4 0.4 C6 B:DG12 3.6 13.9 1.0 C6 B:DG18 3.6 12.7 1.0 C6 B:DG3 3.6 14.1 1.0 C6 B:DG6 3.7 15.9 1.0 C6 B:DG7 3.7 17.3 1.0 C6 B:DG11 3.7 13.6 1.0 N1 B:DG2 3.8 11.8 0.6 N1 B:DG19 3.8 12.6 1.0 N1 B:DG12 3.9 14.1 1.0 N1 B:DG18 3.9 14.1 1.0 N1 B:DG11 4.0 14.3 1.0 N1 B:DG3 4.0 12.2 1.0 N1 B:DG6 4.0 13.3 1.0 N1 B:DG2 4.0 12.8 0.4 N1 B:DG7 4.1 15.6 1.0 C5 B:DG2 4.7 12.3 0.4 C5 B:DG2 4.7 12.1 0.6 C5 B:DG19 4.8 13.2 1.0 C5 B:DG18 4.9 11.1 1.0 C5 B:DG12 4.9 13.4 1.0 C5 B:DG6 4.9 18.0 1.0 C5 B:DG3 4.9 16.6 1.0 C5 B:DG7 4.9 12.9 1.0 C5 B:DG11 4.9 12.7 1.0

Potassium binding site 5 out of 5 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


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 with Bromo Uracil Replacing T8 and T16. within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:12.5 occ:1.00 O6 B:DG20 2.6 14.7 1.0 O6 B:DG13 2.7 13.0 1.0 O6 B:DG4 2.8 17.9 1.0 O6 B:DG9 2.8 17.7 1.0 O6 B:DG19 2.8 13.1 1.0 O6 B:DG12 2.9 14.2 1.0 O6 B:DG7 2.9 12.1 1.0 O6 B:DG3 3.0 16.7 1.0 K B:K101 3.4 12.0 1.0 C6 B:DG20 3.6 22.0 1.0 C6 B:DG12 3.6 13.9 1.0 C6 B:DG13 3.7 18.1 1.0 C6 B:DG4 3.7 16.7 1.0 C6 B:DG19 3.7 14.2 1.0 C6 B:DG9 3.7 16.8 1.0 C6 B:DG7 3.7 17.3 1.0 C6 B:DG3 3.8 14.1 1.0 N1 B:DG4 3.9 20.3 1.0 N1 B:DG13 3.9 19.1 1.0 N1 B:DG9 3.9 20.6 1.0 N1 B:DG12 3.9 14.1 1.0 N1 B:DG20 4.0 12.7 1.0 N1 B:DG19 4.0 12.6 1.0 N1 B:DG7 4.1 15.6 1.0 N1 B:DG3 4.1 12.2 1.0 N6 B:DA22 4.3 21.4 1.0 C6 B:DA22 4.8 28.2 1.0 C5 B:DG12 4.8 13.4 1.0 C5 B:DG7 4.9 12.9 1.0 C5 B:DG19 4.9 13.2 1.0 C5 B:DG20 4.9 11.8 1.0 C5 B:DG4 5.0 14.4 1.0 C5 B:DG13 5.0 15.8 1.0 C5 B:DG9 5.0 17.8 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