Potassium in PDB 4h29: B-Raf Dimer Dna Quadruplex

The structure of B-Raf Dimer Dna Quadruplex, PDB code: 4h29 was solved by D.Wei, G.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.44 / 1.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	33.460, 47.680, 137.320, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.2

The binding sites of Potassium atom in the B-Raf Dimer Dna Quadruplex (pdb code 4h29). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the B-Raf Dimer Dna Quadruplex, PDB code: 4h29:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:30.9 occ:1.00 O6 A:DG17 2.7 33.7 1.0 O6 B:DG8 2.7 22.3 1.0 O6 A:DG12 2.8 24.8 1.0 O6 B:DG11 2.8 37.7 1.0 O6 B:DG12 2.8 21.4 1.0 O6 B:DG17 2.8 32.5 1.0 O6 A:DG11 2.8 32.6 1.0 O6 A:DG8 2.9 33.1 1.0 K A:K102 3.3 32.3 1.0 K A:K104 3.4 33.2 1.0 C6 B:DG11 3.6 33.7 1.0 C6 A:DG11 3.6 35.1 1.0 C6 B:DG8 3.6 30.4 1.0 C6 A:DG17 3.7 24.8 1.0 C6 B:DG12 3.7 26.8 1.0 C6 A:DG12 3.7 30.9 1.0 C6 B:DG17 3.7 30.6 1.0 C6 A:DG8 3.8 30.8 1.0 N1 A:DG11 3.9 25.0 1.0 N1 B:DG12 3.9 18.0 1.0 N1 B:DG11 4.0 29.1 1.0 N1 B:DG17 4.0 36.8 1.0 N1 B:DG8 4.0 27.7 1.0 N1 A:DG17 4.0 27.9 1.0 N1 A:DG12 4.0 19.0 1.0 N1 A:DG8 4.0 30.4 1.0 C5 B:DG11 4.8 31.0 1.0 C5 A:DG11 4.8 31.9 1.0 C5 B:DG8 4.9 29.4 1.0 C5 A:DG17 4.9 28.0 1.0 C5 B:DG17 4.9 33.6 1.0 C5 B:DG12 4.9 24.6 1.0 C5 A:DG12 5.0 20.1 1.0 C5 A:DG8 5.0 29.4 1.0

Potassium binding site 2 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:32.3 occ:1.00 O6 A:DG13 2.7 20.4 1.0 O6 B:DG12 2.7 21.4 1.0 O6 B:DG18 2.8 36.6 1.0 O6 A:DG12 2.8 24.8 1.0 O6 B:DG13 2.9 25.5 1.0 O6 A:DG18 2.9 25.6 1.0 O6 A:DG17 2.9 33.7 1.0 O6 B:DG17 2.9 32.5 1.0 K A:K101 3.3 30.9 1.0 C6 B:DG12 3.6 26.8 1.0 K A:K103 3.6 32.0 1.0 C6 A:DG13 3.7 22.2 1.0 C6 A:DG12 3.7 30.9 1.0 C6 A:DG17 3.7 24.8 1.0 C6 B:DG17 3.7 30.6 1.0 C6 B:DG18 3.7 40.8 1.0 C6 B:DG13 3.7 29.1 1.0 C6 A:DG18 3.7 23.9 1.0 N1 B:DG17 3.9 36.8 1.0 N1 B:DG12 3.9 18.0 1.0 N1 A:DG18 4.0 25.1 1.0 N1 A:DG17 4.0 27.9 1.0 N1 B:DG18 4.0 36.5 1.0 N1 B:DG13 4.0 26.2 1.0 N1 A:DG13 4.0 16.4 1.0 N1 A:DG12 4.1 19.0 1.0 C5 B:DG12 4.7 24.6 1.0 C5 A:DG12 4.8 20.1 1.0 C5 A:DG17 4.9 28.0 1.0 C5 B:DG17 4.9 33.6 1.0 C5 A:DG13 4.9 17.7 1.0 C5 B:DG13 5.0 26.2 1.0 C5 B:DG18 5.0 28.4 1.0

Potassium binding site 3 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:32.0 occ:1.00 O6 B:DG19 2.5 29.9 1.0 O6 A:DG14 2.6 32.7 1.0 O6 B:DG14 2.7 34.3 1.0 O6 A:DG19 2.7 33.7 1.0 O6 A:DG13 2.9 20.4 1.0 O6 B:DG13 2.9 25.5 1.0 O6 B:DG18 3.0 36.6 1.0 O6 A:DG18 3.0 25.6 1.0 C6 B:DG19 3.5 37.2 1.0 K A:K102 3.6 32.3 1.0 C6 A:DG14 3.6 31.5 1.0 C6 B:DG14 3.7 40.7 1.0 C6 A:DG13 3.7 22.2 1.0 C6 A:DG19 3.7 31.8 1.0 C6 B:DG13 3.7 29.1 1.0 C6 A:DG18 3.8 23.9 1.0 C6 B:DG18 3.8 40.8 1.0 N1 B:DG19 3.8 29.3 1.0 N1 A:DG14 3.9 33.1 1.0 N1 B:DG14 3.9 36.9 1.0 N1 A:DG19 4.0 33.5 1.0 N1 A:DG18 4.0 25.1 1.0 N1 B:DG18 4.0 36.5 1.0 N1 A:DG13 4.1 16.4 1.0 N1 B:DG13 4.1 26.2 1.0 C5 A:DG13 4.8 17.7 1.0 C5 B:DG19 4.8 40.6 1.0 C5 B:DG13 4.9 26.2 1.0 C5 A:DG14 4.9 33.5 1.0 C5 A:DG18 4.9 24.7 1.0 C5 B:DG18 5.0 28.4 1.0

Potassium binding site 4 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:33.2 occ:1.00 O6 A:DG7 2.7 32.8 1.0 O6 B:DG7 2.8 28.9 1.0 O6 B:DG10 2.8 37.8 1.0 O6 B:DG11 2.8 37.7 1.0 O6 B:DG8 2.9 22.3 1.0 O6 A:DG8 2.9 33.1 1.0 O6 A:DG11 2.9 32.6 1.0 O6 A:DG10 3.1 43.4 1.0 K A:K101 3.4 30.9 1.0 K B:K101 3.5 36.8 1.0 C6 A:DG7 3.6 33.1 1.0 C6 B:DG10 3.6 32.7 1.0 C6 B:DG7 3.6 23.6 1.0 C6 A:DG8 3.7 30.8 1.0 C6 B:DG8 3.7 30.4 1.0 C6 B:DG11 3.7 33.7 1.0 C6 A:DG11 3.7 35.1 1.0 C6 A:DG10 3.8 32.1 1.0 N1 B:DG10 3.9 29.5 1.0 N1 A:DG8 3.9 30.4 1.0 N1 A:DG7 4.0 28.7 1.0 N1 B:DG7 4.0 22.2 1.0 N1 B:DG8 4.0 27.7 1.0 N1 A:DG11 4.0 25.0 1.0 N1 B:DG11 4.0 29.1 1.0 N1 A:DG10 4.0 36.7 1.0 C5 A:DG7 4.8 32.9 1.0 C5 B:DG10 4.8 33.8 1.0 C5 B:DG7 4.8 28.1 1.0 C5 B:DG8 4.9 29.4 1.0 C5 A:DG8 4.9 29.4 1.0 C5 B:DG11 4.9 31.0 1.0 C5 A:DG11 5.0 31.9 1.0

Potassium binding site 5 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:36.8 occ:1.00 O6 B:DG6 2.5 41.4 1.0 O6 B:DG1 2.7 33.6 1.0 O6 A:DG6 2.7 35.4 1.0 O6 A:DG1 2.8 41.4 1.0 O6 B:DG10 2.8 37.8 1.0 O6 A:DG10 2.8 43.4 1.0 O6 A:DG7 2.9 32.8 1.0 O6 B:DG7 2.9 28.9 1.0 C6 B:DG6 3.4 40.4 1.0 K B:K102 3.5 47.1 1.0 K A:K104 3.5 33.2 1.0 C6 A:DG6 3.5 30.6 1.0 C6 B:DG1 3.6 37.9 1.0 C6 A:DG7 3.7 33.1 1.0 C6 A:DG1 3.7 37.7 1.0 C6 B:DG10 3.7 32.7 1.0 C6 B:DG7 3.7 23.6 1.0 C6 A:DG10 3.8 32.1 1.0 N1 A:DG6 3.9 31.3 1.0 N1 A:DG7 3.9 28.7 1.0 N1 B:DG6 3.9 31.3 1.0 N1 B:DG1 3.9 38.2 1.0 N1 A:DG1 4.0 39.7 1.0 N1 B:DG7 4.0 22.2 1.0 N1 B:DG10 4.1 29.5 1.0 N1 A:DG10 4.1 36.7 1.0 C5 B:DG6 4.6 35.2 1.0 C5 A:DG6 4.8 34.2 1.0 C5 A:DG7 4.9 32.9 1.0 C5 B:DG1 4.9 35.3 1.0 C5 B:DG10 4.9 33.8 1.0 C5 B:DG7 5.0 28.1 1.0 C5 A:DG10 5.0 39.5 1.0 C5 A:DG1 5.0 37.8 1.0

Potassium binding site 6 out of 6 in the B-Raf Dimer Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of B-Raf Dimer Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:47.1 occ:1.00 O6 B:DG5 2.4 46.4 1.0 O6 A:DG5 2.5 41.8 1.0 O6 A:DG2 2.6 53.9 1.0 O6 B:DG2 2.7 49.3 1.0 O6 A:DG1 3.0 41.4 1.0 O6 B:DG1 3.0 33.6 1.0 O6 B:DG6 3.0 41.4 1.0 O6 A:DG6 3.1 35.4 1.0 C6 B:DG5 3.4 48.3 1.0 K B:K101 3.5 36.8 1.0 C6 A:DG5 3.5 41.9 1.0 C6 A:DG2 3.6 50.4 1.0 C6 B:DG2 3.6 43.2 1.0 C6 A:DG1 3.7 37.7 1.0 C6 B:DG1 3.7 37.9 1.0 C6 B:DG6 3.8 40.4 1.0 N1 A:DG2 3.8 48.0 1.0 N1 B:DG5 3.8 43.0 1.0 N1 B:DG2 3.9 43.6 1.0 C6 A:DG6 3.9 30.6 1.0 N1 A:DG5 4.0 39.8 1.0 N1 B:DG6 4.0 31.3 1.0 N2 B:DG3 4.1 64.2 1.0 N1 A:DG1 4.1 39.7 1.0 N1 B:DG1 4.1 38.2 1.0 N1 A:DG6 4.1 31.3 1.0 C5 B:DG5 4.6 44.3 1.0 C5 A:DG5 4.7 42.7 1.0 C5 B:DG1 4.8 35.3 1.0 C5 A:DG1 4.8 37.8 1.0 C5 A:DG2 4.9 51.0 1.0 C5 B:DG6 5.0 35.2 1.0 C5 B:DG2 5.0 38.3 1.0

D.Wei, A.K.Todd, M.Zloh, M.Gunaratnam, G.N.Parkinson, S.Neidle. Crystal Structure of A Promoter Sequence in the B-Raf Gene Reveals An Intertwined Dimer Quadruplex. J.Am.Chem.Soc. V. 135 19319 2013.
ISSN: ISSN 0002-7863
PubMed: 24295054
DOI: 10.1021/JA4101358