Potassium in PDB 7zur: Four Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder

The structure of Four Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 7zur was solved by C.Bazzicalupi, M.Ferraroni, P.Gratteri, F.Papi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 1.60
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.1, 42.1, 34.15, 90, 90, 90
R / Rfree (%)	28.2 / 31

The binding sites of Potassium atom in the Four Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder (pdb code 7zur). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Four Carbons Pendant Pyridine Derivative of the Natural Alkaloid Berberine As Human Telomeric G-Quadruplex Binder, PDB code: 7zur:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Four 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 Four 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:44.3 occ:0.50 O6 A:DG9 3.0 52.2 1.0 O6 A:DG3 3.0 50.6 1.0 O6 A:DG10 3.1 50.2 1.0 O6 A:DG4 3.1 56.1 1.0 K A:K102 3.5 41.6 0.5 H1 A:DG10 3.6 52.8 1.0 H1 A:DG9 3.6 46.0 1.0 H1 A:DG3 3.7 47.9 1.0 H1 A:DG4 3.9 53.4 1.0 C6 A:DG9 3.9 47.0 1.0 C6 A:DG10 3.9 52.1 1.0 C6 A:DG3 3.9 48.7 1.0 C6 A:DG4 4.1 49.0 1.0 N1 A:DG10 4.1 53.0 1.0 N1 A:DG9 4.1 42.7 1.0 N1 A:DG3 4.2 46.6 1.0 N1 A:DG4 4.4 56.2 1.0

Potassium binding site 2 out of 2 in the Four 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 Four 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:41.6 occ:0.50 O6 A:DG11 2.3 55.2 1.0 O6 A:DG10 2.7 50.2 1.0 H1 A:DG11 2.9 52.4 1.0 O6 A:DG5 3.0 52.7 1.0 H1 A:DG10 3.1 52.8 1.0 C6 A:DG11 3.1 43.5 1.0 H1 A:DG5 3.3 54.2 1.0 O6 A:DG4 3.3 56.1 1.0 C6 A:DG10 3.3 52.1 1.0 N1 A:DG11 3.4 54.8 1.0 N1 A:DG10 3.5 53.0 1.0 K A:K101 3.5 44.3 0.5 H1 A:DG4 3.7 53.4 1.0 C6 A:DG5 3.9 51.7 1.0 N1 A:DG5 3.9 53.7 1.0 C6 A:DG4 4.1 49.0 1.0 N1 A:DG4 4.2 56.2 1.0 C5 A:DG11 4.5 57.0 1.0 C5 A:DG10 4.5 53.9 1.0 C2 A:DG11 4.7 52.7 1.0 C2 A:DG10 4.7 51.3 1.0 H21 A:DG11 4.8 56.7 1.0 H21 A:DG10 4.9 54.0 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