Potassium in PDB 6ip3: Structure of Human Telomeric Dna at 1.4 Angstroms Resolution

The structure of Structure of Human Telomeric Dna at 1.4 Angstroms Resolution, PDB code: 6ip3 was solved by K.Saikrishnan, A.Nuthanakanti, S.G.Srivatsan, I.Ahmad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.42 / 1.40
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	56.839, 56.839, 42.411, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 17.3

The binding sites of Potassium atom in the Structure of Human Telomeric Dna at 1.4 Angstroms Resolution (pdb code 6ip3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Structure of Human Telomeric Dna at 1.4 Angstroms Resolution, PDB code: 6ip3:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Structure of Human Telomeric Dna at 1.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Human Telomeric Dna at 1.4 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:12.2 occ:1.00 O6 A:DG4 2.6 13.1 1.0 O6 A:DG22 2.7 13.3 1.0 O6 A:DG16 2.7 14.1 1.0 O6 A:DG10 2.7 13.3 1.0 O6 A:DG3 2.9 11.3 0.5 O6 A:DG21 2.9 12.2 1.0 O6 A:DG9 2.9 12.3 1.0 O6 A:DG15 3.0 13.0 1.0 O6 A:DG3 3.2 13.2 0.5 H1 A:DG16 3.4 16.6 1.0 H1 A:DG22 3.4 17.1 1.0 K A:K102 3.4 11.0 1.0 H1 A:DG4 3.4 16.0 1.0 H1 A:DG10 3.5 15.4 1.0 H1 A:DG15 3.6 14.4 1.0 C6 A:DG22 3.6 13.7 1.0 C6 A:DG4 3.6 12.3 1.0 H1 A:DG3 3.7 14.7 0.5 H1 A:DG21 3.7 14.7 1.0 C6 A:DG16 3.7 13.7 1.0 C6 A:DG3 3.7 10.8 0.5 H1 A:DG9 3.7 13.7 1.0 C6 A:DG9 3.7 11.4 1.0 C6 A:DG10 3.7 13.2 1.0 C6 A:DG21 3.7 11.7 1.0 C6 A:DG15 3.7 12.8 1.0 H1 A:DG3 3.7 13.6 0.5 C6 A:DG3 3.9 12.2 0.5 N1 A:DG22 3.9 14.2 1.0 N1 A:DG4 3.9 13.3 1.0 N1 A:DG16 3.9 13.8 1.0 N1 A:DG10 4.0 12.8 1.0 N1 A:DG15 4.0 12.0 1.0 N1 A:DG3 4.0 12.3 0.5 N1 A:DG9 4.0 11.4 1.0 N1 A:DG21 4.0 12.3 1.0 N1 A:DG3 4.1 11.3 0.5 C5 A:DG9 4.8 11.7 1.0 C5 A:DG3 4.8 12.7 0.5 C5 A:DG15 4.9 12.0 1.0 C5 A:DG21 4.9 12.3 1.0 C5 A:DG22 4.9 14.0 1.0 C5 A:DG4 5.0 14.1 1.0 C5 A:DG3 5.0 11.2 0.5 C5 A:DG16 5.0 14.6 1.0

Potassium binding site 2 out of 3 in the Structure of Human Telomeric Dna at 1.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Human Telomeric Dna at 1.4 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:11.0 occ:1.00 O6 A:DG14 2.7 13.2 0.7 O6 A:DG3 2.7 13.2 0.5 O6 A:DG15 2.7 13.0 1.0 O6 A:DG3 2.7 11.3 0.5 O6 A:DG21 2.7 12.2 1.0 O6 A:DG2 2.7 12.3 0.5 O6 A:DG9 2.8 12.3 1.0 O6 A:DG20 2.8 11.8 1.0 O6 A:DG8 2.8 11.1 1.0 O6 A:DG2 2.9 8.5 0.5 O6 A:DG14 3.0 8.0 0.3 K A:K103 3.3 12.6 0.5 K A:K101 3.4 12.2 1.0 H1 A:DG2 3.4 14.0 0.5 H1 A:DG14 3.5 12.8 0.7 H1 A:DG21 3.5 14.7 1.0 H1 A:DG15 3.5 14.4 1.0 H1 A:DG8 3.5 12.8 1.0 C6 A:DG14 3.6 11.5 0.7 H1 A:DG9 3.6 13.7 1.0 H1 A:DG3 3.6 13.6 0.5 H1 A:DG20 3.6 13.7 1.0 H1 A:DG3 3.6 14.7 0.5 C6 A:DG8 3.6 10.4 1.0 C6 A:DG21 3.6 11.7 1.0 H1 A:DG2 3.6 11.2 0.5 C6 A:DG15 3.7 12.8 1.0 C6 A:DG2 3.7 11.6 0.5 C6 A:DG3 3.7 12.2 0.5 C6 A:DG3 3.7 10.8 0.5 C6 A:DG20 3.7 11.6 1.0 C6 A:DG9 3.7 11.4 1.0 C6 A:DG14 3.7 11.2 0.3 C6 A:DG2 3.8 10.1 0.5 N1 A:DG14 3.9 10.7 0.7 N1 A:DG8 3.9 10.7 1.0 N1 A:DG21 3.9 12.3 1.0 N1 A:DG2 3.9 11.7 0.5 N1 A:DG15 3.9 12.0 1.0 N1 A:DG14 4.0 12.1 0.3 N1 A:DG20 4.0 11.4 1.0 N1 A:DG3 4.0 12.3 0.5 N1 A:DG3 4.0 11.3 0.5 N1 A:DG9 4.0 11.4 1.0 N1 A:DG2 4.0 9.3 0.5 C5 A:DG14 4.8 10.5 0.7 C5 A:DG8 4.8 11.4 1.0 C5 A:DG21 4.9 12.3 1.0 C5 A:DG20 4.9 12.4 1.0 C5 A:DG3 4.9 12.7 0.5 C5 A:DG15 4.9 12.0 1.0 C5 A:DG14 4.9 12.8 0.3 C5 A:DG2 4.9 12.5 0.5 C5 A:DG3 4.9 11.2 0.5 C5 A:DG2 5.0 11.8 0.5 C5 A:DG9 5.0 11.7 1.0

Potassium binding site 3 out of 3 in the Structure of Human Telomeric Dna at 1.4 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Human Telomeric Dna at 1.4 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:12.6 occ:0.50 O6 A:DG2 2.7 8.5 0.5 O6 A:DG14 2.7 8.0 0.3 O6 A:DG20 2.8 11.8 1.0 O6 A:DG8 2.8 11.1 1.0 O6 A:DG14 2.9 13.2 0.7 O6 A:DG2 2.9 12.3 0.5 K A:K102 3.3 11.0 1.0 H1 A:DG20 3.5 13.7 1.0 H1 A:DG2 3.5 11.2 0.5 H1 A:DG14 3.5 12.8 0.7 C6 A:DG2 3.6 10.1 0.5 H1 A:DG2 3.6 14.0 0.5 H1 A:DG8 3.6 12.8 1.0 C6 A:DG20 3.6 11.6 1.0 C6 A:DG14 3.6 11.2 0.3 C6 A:DG2 3.7 11.6 0.5 C6 A:DG14 3.7 11.5 0.7 C6 A:DG8 3.7 10.4 1.0 N1 A:DG14 3.9 12.1 0.3 N1 A:DG2 3.9 9.3 0.5 N1 A:DG20 3.9 11.4 1.0 N1 A:DG2 4.0 11.7 0.5 N1 A:DG14 4.0 10.7 0.7 N1 A:DG8 4.0 10.7 1.0 C5 A:DG2 4.8 11.8 0.5 C5 A:DG2 4.8 12.5 0.5 C5 A:DG20 4.9 12.4 1.0 C5 A:DG14 4.9 12.8 0.3 C5 A:DG14 4.9 10.5 0.7 C5 A:DG8 5.0 11.4 1.0

A.Nuthanakanti, I.Ahmed, S.Y.Khatik, K.Saikrishnan, S.G.Srivatsan. Probing G-Quadruplex Topologies and Recognition Concurrently in Real Time and 3D Using A Dual-App Nucleoside Probe. Nucleic Acids Res. V. 47 6059 2019.
ISSN: ESSN 1362-4962
PubMed: 31106340
DOI: 10.1093/NAR/GKZ419