Potassium in PDB 3r6r: Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution

The structure of Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution, PDB code: 3r6r was solved by M.Ferraroni, C.Bazzicalupi, P.Gratteri, A.R.Bilia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	65.620, 65.620, 41.810, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 25.2

The binding sites of Potassium atom in the Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution (pdb code 3r6r). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution, PDB code: 3r6r:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:K1 b:23.2 occ:1.00 O6 A:DG10 2.7 17.1 1.0 O6 A:DG5 2.8 18.0 1.0 O6 A:DG11 2.8 17.3 1.0 O6 A:DG17 2.8 18.0 1.0 O6 A:DG16 2.9 20.8 1.0 O6 A:DG23 2.9 17.9 1.0 O6 A:DG22 2.9 18.4 1.0 O6 A:DG4 3.0 23.4 1.0 O A:HOH38 3.3 41.2 1.0 K A:K24 3.5 22.1 1.0 C6 A:DG10 3.5 16.0 1.0 C6 A:DG5 3.7 18.3 1.0 C6 A:DG16 3.7 19.3 1.0 C6 A:DG11 3.7 17.6 1.0 C6 A:DG17 3.7 18.9 1.0 C6 A:DG4 3.7 21.8 1.0 C6 A:DG23 3.8 19.0 1.0 C6 A:DG22 3.8 17.9 1.0 N1 A:DG5 3.9 16.5 1.0 N1 A:DG10 3.9 15.2 1.0 N1 A:DG4 3.9 22.0 1.0 N1 A:DG16 4.0 19.4 1.0 N1 A:DG17 4.0 17.0 1.0 N1 A:DG11 4.0 17.4 1.0 N1 A:DG23 4.0 18.3 1.0 N1 A:DG22 4.1 17.5 1.0 C5 A:DG10 4.7 15.2 1.0 C5 A:DG16 4.9 19.3 1.0 C5 A:DG4 5.0 22.2 1.0 C5 A:DG5 5.0 19.5 1.0 C5 A:DG22 5.0 18.2 1.0 C5 A:DG11 5.0 17.4 1.0

Potassium binding site 2 out of 2 in the Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Complex of An Intramolecular Human Telomeric Dna with Berberine Formed in K+ Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:K24 b:22.1 occ:1.00 O6 A:DG3 2.7 20.1 1.0 O6 A:DG15 2.7 18.7 1.0 O6 A:DG21 2.7 15.5 1.0 O6 A:DG10 2.8 17.1 1.0 O6 A:DG9 2.8 17.6 1.0 O6 A:DG22 2.9 18.4 1.0 O6 A:DG16 2.9 20.8 1.0 O6 A:DG4 2.9 23.4 1.0 K A:K1 3.5 23.2 1.0 C6 A:DG15 3.6 17.8 1.0 C6 A:DG3 3.6 19.5 1.0 C6 A:DG21 3.6 14.5 1.0 C6 A:DG9 3.7 16.9 1.0 C6 A:DG10 3.7 16.0 1.0 C6 A:DG16 3.7 19.3 1.0 C6 A:DG22 3.8 17.9 1.0 C6 A:DG4 3.8 21.8 1.0 N1 A:DG15 3.8 17.2 1.0 N1 A:DG3 3.8 18.4 1.0 N1 A:DG9 3.9 16.0 1.0 N1 A:DG21 3.9 13.0 1.0 N1 A:DG16 4.0 19.4 1.0 N1 A:DG4 4.0 22.0 1.0 N1 A:DG10 4.0 15.2 1.0 N1 A:DG22 4.1 17.5 1.0 C5 A:DG15 4.8 17.5 1.0 C5 A:DG21 4.8 15.3 1.0 C5 A:DG3 4.8 20.7 1.0 C5 A:DG9 4.9 17.1 1.0 C5 A:DG16 5.0 19.3 1.0 C5 A:DG10 5.0 15.2 1.0

C.Bazzicalupi, M.Ferraroni, A.R.Bilia, F.Scheggi, P.Gratteri. The Crystal Structure of Human Telomeric Dna Complexed with Berberine: An Interesting Case of Stacked Ligand to G-Tetrad Ratio Higher Than 1:1. Nucleic Acids Res. V. 41 632 2013.
ISSN: ISSN 0305-1048
PubMed: 23104378
DOI: 10.1093/NAR/GKS1001