Potassium in PDB 8aad: Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder

The structure of Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 8aad was solved by M.Ferraroni, C.Bazzicalupi, P.Gratteri, F.Papi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.04
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.68, 41.68, 34.31, 90, 90, 90
R / Rfree (%)	25.9 / 30.6

The binding sites of Potassium atom in the Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder (pdb code 8aad). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 8aad:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:8.5 occ:0.50 O6 A:DG5 2.8 16.1 1.0 O6 A:DG4 2.9 15.8 1.0 O6 A:DG11 3.0 17.9 1.0 O6 A:DG10 3.2 16.5 1.0 K A:K102 3.6 10.1 0.5 C6 A:DG4 3.8 17.7 1.0 C6 A:DG5 3.9 20.8 1.0 C6 A:DG11 4.0 19.3 1.0 C6 A:DG10 4.0 17.7 1.0 N1 A:DG11 4.2 17.8 1.0 N1 A:DG4 4.2 17.1 1.0 N1 A:DG10 4.3 18.4 1.0 N1 A:DG5 4.3 18.3 1.0 C5 A:DG4 4.9 20.7 1.0

Potassium binding site 2 out of 2 in the Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Two Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:10.1 occ:0.50 O6 A:DG3 2.6 21.0 1.0 O6 A:DG4 3.0 15.8 1.0 O6 A:DG9 3.0 18.4 1.0 O6 A:DG10 3.1 16.5 1.0 C6 A:DG3 3.5 21.3 1.0 K A:K101 3.6 8.5 0.5 C6 A:DG9 3.8 20.3 1.0 N1 A:DG3 3.9 18.0 1.0 C6 A:DG4 3.9 17.7 1.0 C6 A:DG10 3.9 17.7 1.0 N1 A:DG9 4.0 17.4 1.0 N1 A:DG10 4.2 18.4 1.0 N1 A:DG4 4.3 17.1 1.0 N6 A:DA2 4.7 28.8 1.0 C5 A:DG3 4.8 23.5 1.0

C.Bazzicalupi, A.Bonardi, T.Biver, M.Ferraroni, F.Papi, M.Savastano, P.Lombardi, P.Gratteri. Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and in Silico Analysis. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36430540
DOI: 10.3390/IJMS232214061