Potassium in PDB 5ua3: Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge

The structure of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge, PDB code: 5ua3 was solved by M.Meier, M.D.Mcdougall, N.J.Krahn, A.Moya-Torres, E.K.S.Mcrae, E.P.Booy, T.R.Patel, S.A.Mckenna, J.Stetefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.49 / 1.88
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.103, 33.100, 33.282, 64.65, 78.64, 81.78
R / Rfree (%)	22.7 / 24.7

The binding sites of Potassium atom in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge (pdb code 5ua3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge, PDB code: 5ua3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:30.2 occ:1.00 O6 A:DG3 2.5 23.2 1.0 O6 A:DG9 2.5 24.2 1.0 O6 A:DG13 2.6 23.3 1.0 O6 A:DG17 2.7 23.4 1.0 O6 A:DG16 2.8 23.6 1.0 O6 A:DG12 2.9 22.5 1.0 O6 A:DG8 3.0 23.2 1.0 O6 A:DG2 3.1 27.0 1.0 K A:K102 3.4 25.7 1.0 C6 A:DG3 3.5 24.3 1.0 C6 A:DG9 3.5 25.5 1.0 C6 A:DG13 3.6 24.1 1.0 C6 A:DG12 3.7 22.7 1.0 C6 A:DG17 3.7 24.5 1.0 C6 A:DG16 3.7 24.1 1.0 N1 A:DG3 3.8 23.9 1.0 N1 A:DG9 3.8 24.9 1.0 C6 A:DG2 3.9 27.2 1.0 C6 A:DG8 3.9 24.7 1.0 N1 A:DG13 3.9 24.0 1.0 N1 A:DG12 4.0 22.4 1.0 N1 A:DG17 4.0 25.3 1.0 N1 A:DG16 4.1 24.6 1.0 N1 A:DG8 4.2 24.1 1.0 N1 A:DG2 4.2 27.3 1.0 C5 A:DG12 4.8 23.9 1.0 C5 A:DG3 4.8 26.1 1.0 C5 A:DG9 4.8 26.6 1.0 C5 A:DG16 4.9 24.8 1.0 C5 A:DG13 4.9 25.2 1.0 C5 A:DG17 4.9 25.7 1.0 C5 A:DG2 5.0 29.1 1.0

Potassium binding site 2 out of 5 in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:25.7 occ:1.00 O6 A:DG12 2.6 22.5 1.0 O6 A:DG2 2.7 27.0 1.0 O6 A:DG8 2.7 23.2 1.0 O6 A:DG16 2.7 23.6 1.0 O6 A:DG1 2.8 21.1 1.0 O6 A:DG6 2.8 22.0 1.0 O6 A:DG15 2.8 21.4 1.0 O6 A:DG11 2.9 22.2 1.0 K A:K103 3.3 21.0 1.0 K A:K101 3.4 30.2 1.0 C6 A:DG12 3.6 22.7 1.0 C6 A:DG8 3.6 24.7 1.0 C6 A:DG1 3.6 22.2 1.0 C6 A:DG16 3.6 24.1 1.0 C6 A:DG2 3.6 27.2 1.0 C6 A:DG15 3.7 21.1 1.0 C6 A:DG11 3.7 22.3 1.0 C6 A:DG6 3.7 23.4 1.0 N1 A:DG12 3.9 22.4 1.0 N1 A:DG2 4.0 27.3 1.0 N1 A:DG8 4.0 24.1 1.0 N1 A:DG1 4.0 22.7 1.0 N1 A:DG16 4.0 24.6 1.0 N1 A:DG15 4.0 21.2 1.0 N1 A:DG11 4.0 22.4 1.0 N1 A:DG6 4.1 24.0 1.0 C5 A:DG12 4.8 23.9 1.0 C5 A:DG8 4.8 26.1 1.0 C5 A:DG1 4.8 23.6 1.0 C5 A:DG16 4.9 24.8 1.0 C5 A:DG11 4.9 23.5 1.0 C5 A:DG2 4.9 29.1 1.0 C5 A:DG15 5.0 21.9 1.0 C5 A:DG6 5.0 25.4 1.0 O6 A:DG3 5.0 23.2 1.0

Potassium binding site 3 out of 5 in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:21.0 occ:1.00 O6 B:DG1 2.7 19.8 1.0 O6 A:DG1 2.8 21.1 1.0 O6 B:DG11 2.8 21.5 1.0 O6 A:DG11 2.8 22.2 1.0 O6 A:DG15 2.8 21.4 1.0 O6 A:DG6 2.8 22.0 1.0 O6 B:DG15 2.8 22.4 1.0 O6 B:DG6 2.9 22.9 1.0 K B:K101 3.3 25.2 1.0 K A:K102 3.3 25.7 1.0 C6 B:DG1 3.7 21.8 1.0 C6 A:DG1 3.7 22.2 1.0 C6 B:DG11 3.7 21.4 1.0 C6 A:DG11 3.7 22.3 1.0 C6 A:DG6 3.7 23.4 1.0 C6 A:DG15 3.7 21.1 1.0 C6 B:DG15 3.7 22.5 1.0 C6 B:DG6 3.7 24.9 1.0 N1 A:DG1 3.9 22.7 1.0 N1 A:DG11 4.0 22.4 1.0 N1 B:DG15 4.0 22.9 1.0 N1 B:DG1 4.0 22.1 1.0 N1 A:DG6 4.0 24.0 1.0 N1 B:DG11 4.0 21.0 1.0 N1 A:DG15 4.0 21.2 1.0 N1 B:DG6 4.0 24.8 1.0 C5 B:DG1 4.9 23.1 1.0 C5 A:DG15 4.9 21.9 1.0 C5 A:DG6 4.9 25.4 1.0 C5 A:DG1 4.9 23.6 1.0 C5 B:DG11 4.9 22.3 1.0 C5 A:DG11 4.9 23.5 1.0 C5 B:DG15 4.9 23.3 1.0 C5 B:DG6 5.0 27.1 1.0

Potassium binding site 4 out of 5 in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:25.2 occ:1.00 O6 B:DG12 2.6 24.5 1.0 O6 B:DG16 2.7 25.2 1.0 O6 B:DG2 2.7 24.7 1.0 O6 B:DG8 2.7 23.9 1.0 O6 B:DG11 2.8 21.5 1.0 O6 B:DG6 2.8 22.9 1.0 O6 B:DG1 2.8 19.8 1.0 O6 B:DG15 2.8 22.4 1.0 K A:K103 3.3 21.0 1.0 K B:K102 3.5 29.8 1.0 C6 B:DG12 3.6 25.3 1.0 C6 B:DG8 3.6 24.9 1.0 C6 B:DG16 3.6 26.2 1.0 C6 B:DG11 3.7 21.4 1.0 C6 B:DG1 3.7 21.8 1.0 C6 B:DG2 3.7 25.4 1.0 C6 B:DG6 3.7 24.9 1.0 C6 B:DG15 3.7 22.5 1.0 N1 B:DG12 3.9 25.0 1.0 N1 B:DG8 3.9 24.5 1.0 N1 B:DG2 4.0 25.2 1.0 N1 B:DG16 4.0 26.9 1.0 N1 B:DG1 4.0 22.1 1.0 N1 B:DG11 4.0 21.0 1.0 N1 B:DG15 4.1 22.9 1.0 N1 B:DG6 4.1 24.8 1.0 C5 B:DG12 4.8 25.9 1.0 C5 B:DG11 4.8 22.3 1.0 C5 B:DG8 4.8 26.7 1.0 C5 B:DG1 4.9 23.1 1.0 C5 B:DG16 4.9 26.9 1.0 C5 B:DG6 4.9 27.1 1.0 C5 B:DG15 4.9 23.3 1.0 O6 B:DG3 5.0 25.9 1.0 C5 B:DG2 5.0 27.0 1.0

Potassium binding site 5 out of 5 in the Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Dna G-Quadruplex with A Cytosine Bulge within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:29.8 occ:1.00 O6 B:DG3 2.5 25.9 1.0 O6 B:DG17 2.5 25.3 1.0 O6 B:DG13 2.5 24.0 1.0 O6 B:DG9 2.6 27.0 1.0 O6 B:DG12 2.9 24.5 1.0 O6 B:DG16 3.0 25.2 1.0 O6 B:DG8 3.1 23.9 1.0 O6 B:DG2 3.2 24.7 1.0 C6 B:DG3 3.5 27.7 1.0 K B:K101 3.5 25.2 1.0 C6 B:DG17 3.5 27.4 1.0 C6 B:DG13 3.5 25.1 1.0 C6 B:DG9 3.6 27.2 1.0 C6 B:DG12 3.7 25.3 1.0 N1 B:DG3 3.8 27.8 1.0 N1 B:DG9 3.8 26.8 1.0 C6 B:DG16 3.8 26.2 1.0 N1 B:DG13 3.9 25.5 1.0 C6 B:DG8 3.9 24.9 1.0 N1 B:DG17 3.9 28.0 1.0 C6 B:DG2 3.9 25.4 1.0 N1 B:DG12 4.0 25.0 1.0 N1 B:DG8 4.1 24.5 1.0 N1 B:DG16 4.2 26.9 1.0 N1 B:DG2 4.3 25.2 1.0 C5 B:DG12 4.8 25.9 1.0 C5 B:DG17 4.8 29.1 1.0 C5 B:DG3 4.8 29.8 1.0 C5 B:DG13 4.9 26.2 1.0 C5 B:DG9 4.9 28.6 1.0 C5 B:DG16 5.0 26.9 1.0

M.Meier, A.Moya-Torres, N.J.Krahn, M.D.Mcdougall, G.L.Orriss, E.K.S.Mcrae, E.P.Booy, K.Mceleney, T.R.Patel, S.A.Mckenna, J.Stetefeld. Structure and Hydrodynamics of A Dna G-Quadruplex with A Cytosine Bulge. Nucleic Acids Res. V. 46 5319 2018.
ISSN: ESSN 1362-4962
PubMed: 29718405
DOI: 10.1093/NAR/GKY307