Potassium in PDB 6s15: Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder

The structure of Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 6s15 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)	35.35 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.250, 41.250, 68.600, 90.00, 90.00, 90.00
R / Rfree (%)	26.6 / 29.4

The binding sites of Potassium atom in the Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder (pdb code 6s15). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 6s15:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the 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 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:19.0 occ:1.00 O6 A:DG3 2.6 20.2 1.0 O6 B:DG21 2.7 21.8 1.0 O6 B:DG15 2.7 22.1 1.0 O6 A:DG9 2.8 22.9 1.0 O6 A:DG10 2.8 19.0 1.0 O6 A:DG4 2.9 20.3 1.0 O6 B:DG22 2.9 21.1 1.0 O6 B:DG16 2.9 19.2 1.0 C6 A:DG3 3.5 21.4 1.0 C6 B:DG21 3.5 22.8 1.0 K A:K102 3.6 19.4 1.0 C6 A:DG9 3.6 20.9 1.0 C6 B:DG15 3.6 21.5 1.0 C6 A:DG10 3.7 23.8 1.0 C6 B:DG22 3.8 22.7 1.0 N1 B:DG21 3.8 21.8 1.0 C6 A:DG4 3.8 20.0 1.0 N1 A:DG3 3.8 20.5 1.0 C6 B:DG16 3.8 21.4 1.0 N1 A:DG9 3.9 23.4 1.0 N1 B:DG15 3.9 22.8 1.0 N1 A:DG10 4.0 22.7 1.0 N1 B:DG22 4.0 19.5 1.0 N1 A:DG4 4.1 19.9 1.0 N1 B:DG16 4.2 19.6 1.0 N6 A:DA2 4.8 29.7 1.0 C5 A:DG3 4.8 22.3 1.0 C5 B:DG21 4.8 24.1 1.0 C5 A:DG9 4.9 22.5 1.0 C5 B:DG15 4.9 22.8 1.0 C5 A:DG10 4.9 21.1 1.0 C5 B:DG22 5.0 19.4 1.0

Potassium binding site 2 out of 2 in the 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 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:19.4 occ:1.00 O6 A:DG11 2.6 21.3 1.0 O6 B:DG17 2.7 21.9 1.0 O6 B:DG23 2.7 23.8 1.0 O6 A:DG5 2.7 28.9 1.0 O6 A:DG4 2.9 20.3 1.0 O6 B:DG22 2.9 21.1 1.0 O6 A:DG10 2.9 19.0 1.0 O6 B:DG16 3.0 19.2 1.0 K A:K101 3.6 19.0 1.0 C6 A:DG11 3.6 22.2 1.0 C6 B:DG22 3.7 22.7 1.0 C6 B:DG23 3.7 21.0 1.0 C6 A:DG4 3.7 20.0 1.0 C6 A:DG10 3.7 23.8 1.0 C6 B:DG17 3.7 22.9 1.0 C6 A:DG5 3.7 24.1 1.0 C6 B:DG16 3.8 21.4 1.0 N1 A:DG11 3.9 25.7 1.0 N1 B:DG23 3.9 19.6 1.0 N1 B:DG22 3.9 19.5 1.0 N1 A:DG5 3.9 24.7 1.0 N1 B:DG17 4.0 19.7 1.0 N1 A:DG4 4.0 19.9 1.0 N1 A:DG10 4.0 22.7 1.0 N1 B:DG16 4.1 19.6 1.0 C5 A:DG4 4.8 21.5 1.0 C5 A:DG10 4.8 21.1 1.0 C5 B:DG22 4.9 19.4 1.0 C5 A:DG11 4.9 23.9 1.0 C5 B:DG16 4.9 20.8 1.0 C5 B:DG23 5.0 21.3 1.0

F.Papi, C.Bazzicalupi, M.Ferraroni, G.Ciolli, P.Lombardi, A.Y.Khan, G.S.Kumar, P.Gratteri. Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G4-Dna Binder: A Solution and Solid-State Study. Acs Med.Chem.Lett. V. 11 645 2020.
ISSN: ISSN 1948-5875
PubMed: 32435365
DOI: 10.1021/ACSMEDCHEMLETT.9B00516