Bromine 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:

Potassium

(K)

5 atoms

The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine where determined in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16., PDB code: 6wck:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br8 b:81.7 occ:1.00 BR A:BRU8 0.0 81.7 1.0 C5 A:BRU8 1.9 26.9 1.0 C4 A:BRU8 2.9 18.8 1.0 C6 A:BRU8 3.0 25.0 1.0 O4 A:BRU8 3.1 20.7 1.0 O A:HOH239 3.6 36.5 1.0 O3' A:DG4 3.8 23.2 1.0 O A:HOH225 4.0 23.0 1.0 C2' A:DG4 4.0 20.6 1.0 C1' A:DG4 4.2 18.2 1.0 N3 A:BRU8 4.3 16.1 1.0 N1 A:BRU8 4.3 18.8 1.0 OP2 A:DC5 4.4 25.7 1.0 C3' A:DG4 4.5 24.0 1.0 N3 A:DG4 4.7 16.3 1.0 P A:DC5 4.8 25.3 1.0 N9 A:DG4 4.8 18.0 1.0 C2 A:BRU8 4.9 17.4 1.0

Bromine binding site 2 out of 4 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br16 b:0.1 occ:1.00 BR A:BRU16 0.0 0.1 1.0 C5 A:BRU16 1.9 0.6 1.0 C6 A:BRU16 2.9 98.4 1.0 C4 A:BRU16 3.0 0.7 1.0 O4 A:BRU16 3.2 0.9 1.0 N6 B:DA1 3.6 35.6 0.6 N6 A:DA17 3.9 32.9 1.0 N7 A:DA17 4.0 25.9 1.0 N6 B:DA1 4.1 34.5 0.4 O3' A:DA15 4.1 63.5 1.0 N1 A:BRU16 4.3 93.9 1.0 N3 A:BRU16 4.4 0.4 1.0 C1' A:DA15 4.4 38.2 1.0 O5' A:BRU16 4.6 65.5 1.0 OP1 A:BRU16 4.7 71.6 1.0 C5 A:DA17 4.7 22.9 1.0 C6 A:DA17 4.7 28.6 1.0 P A:BRU16 4.8 75.9 1.0 C6 B:DA1 4.8 28.2 0.6 C2' A:DA15 4.8 41.6 1.0 C2 A:BRU16 4.9 0.9 1.0

Bromine binding site 3 out of 4 in the Kras G-Quadruplex G16T Mutant with Bromo Uracil Replacing T8 and T16.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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 B:Br8 b:77.2 occ:1.00 BR B:BRU8 0.0 77.2 1.0 C5 B:BRU8 1.9 27.5 1.0 C4 B:BRU8 2.9 25.6 1.0 C6 B:BRU8 3.0 22.5 1.0 O4 B:BRU8 3.1 26.5 1.0 O B:HOH246 3.2 32.4 1.0 O B:HOH208 3.8 23.7 1.0 O B:HOH238 3.8 34.7 1.0 O3' B:DG4 3.9 25.3 1.0 C2' B:DG4 3.9 17.8 1.0 C1' B:DG4 4.1 21.9 1.0 N3 B:BRU8 4.3 22.0 1.0 N1 B:BRU8 4.3 19.8 1.0 C3' B:DG4 4.5 19.0 1.0 N3 B:DG4 4.7 18.9 1.0 OP2 B:DC5 4.7 28.6 1.0 N9 B:DG4 4.7 20.0 1.0 C2 B:BRU8 4.8 18.7 1.0 C4 B:DG4 5.0 15.1 1.0 P B:DC5 5.0 31.4 1.0

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


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br16 b:0.8 occ:1.00 BR B:BRU16 0.0 0.8 1.0 C5 B:BRU16 1.9 0.2 1.0 C4 B:BRU16 3.0 0.5 1.0 C6 B:BRU16 3.0 0.7 1.0 O4 B:BRU16 3.1 0.5 1.0 N6 A:DA1 3.7 35.8 0.5 N6 A:DA1 4.1 33.6 0.5 N3 B:BRU16 4.3 0.3 1.0 N1 B:BRU16 4.3 0.2 1.0 C2 B:BRU16 4.9 0.6 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