Potassium in PDB 5cdb: Structure of the Complex of A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative

The structure of Structure of the Complex of A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative, PDB code: 5cdb 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)	35.62 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.132, 41.132, 71.204, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.4

The binding sites of Potassium atom in the Structure of the Complex of A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative (pdb code 5cdb). 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 A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative, PDB code: 5cdb:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of the Complex of A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative


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 A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:33.9 occ:1.00 O6 B:DG17 2.7 36.1 1.0 O6 B:DG23 2.7 34.4 1.0 O6 A:DG5 2.7 33.4 1.0 O6 A:DG11 2.7 34.4 1.0 O6 B:DG22 2.9 32.6 1.0 O6 A:DG10 2.9 32.9 1.0 O6 B:DG16 2.9 32.5 1.0 O6 A:DG4 2.9 30.8 1.0 K B:K101 3.6 33.0 1.0 C6 B:DG17 3.6 38.5 1.0 C6 B:DG22 3.6 31.0 1.0 C6 B:DG23 3.7 33.0 1.0 C6 A:DG5 3.7 30.9 1.0 C6 A:DG11 3.7 37.0 1.0 C6 B:DG16 3.7 36.2 1.0 C6 A:DG10 3.7 32.4 1.0 C6 A:DG4 3.7 29.5 1.0 N1 B:DG17 3.8 35.5 1.0 N1 B:DG22 3.9 31.9 1.0 N1 A:DG5 3.9 31.5 1.0 N1 A:DG10 3.9 33.0 1.0 N1 A:DG11 3.9 37.1 1.0 N1 B:DG23 4.0 32.7 1.0 N1 B:DG16 4.0 34.3 1.0 N1 A:DG4 4.1 29.3 1.0 C5 B:DG22 4.8 33.0 1.0 C5 B:DG16 4.8 40.0 1.0 C5 A:DG4 4.9 32.2 1.0 C5 A:DG10 4.9 32.6 1.0 C5 B:DG17 4.9 40.8 1.0 C5 A:DG11 5.0 35.3 1.0 C5 B:DG23 5.0 34.8 1.0 C5 A:DG5 5.0 31.7 1.0

Potassium binding site 2 out of 2 in the Structure of the Complex of A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative


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 A Bimolecular Human Telomeric Dna with A 13-Diphenylalkyl Berberine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:33.0 occ:1.00 O6 B:DG15 2.6 40.9 1.0 O6 A:DG3 2.7 36.7 1.0 O6 A:DG9 2.8 34.2 1.0 O6 B:DG21 2.8 33.9 1.0 O6 A:DG10 2.8 32.9 1.0 O6 B:DG16 2.9 32.5 1.0 O6 A:DG4 2.9 30.8 1.0 O6 B:DG22 2.9 32.6 1.0 C6 B:DG15 3.5 39.1 1.0 C6 A:DG3 3.5 34.8 1.0 K A:K101 3.6 33.9 1.0 C6 A:DG9 3.6 30.8 1.0 C6 B:DG21 3.6 35.6 1.0 C6 A:DG10 3.7 32.4 1.0 C6 A:DG4 3.7 29.5 1.0 C6 B:DG16 3.8 36.2 1.0 C6 B:DG22 3.8 31.0 1.0 N1 B:DG15 3.8 36.5 1.0 N1 A:DG9 3.8 30.6 1.0 N1 B:DG21 3.8 34.5 1.0 N1 A:DG3 3.9 34.0 1.0 N1 A:DG4 4.0 29.3 1.0 N1 A:DG10 4.1 33.0 1.0 N1 B:DG22 4.1 31.9 1.0 N1 B:DG16 4.1 34.3 1.0 N6 B:DA14 4.5 44.5 1.0 C5 B:DG15 4.7 39.3 1.0 C5 A:DG3 4.8 37.5 1.0 C5 A:DG9 4.8 32.5 1.0 C5 B:DG21 4.9 37.4 1.0 C5 A:DG10 4.9 32.6 1.0 N6 A:DA2 5.0 44.9 1.0 C5 A:DG4 5.0 32.2 1.0

M.Ferraroni, C.Bazzicalupi, F.Papi, G.Fiorillo, L.M.Guaman-Ortiz, A.Nocentini, A.I.Scovassi, P.Lombardi, P.Gratteri. Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-Quadruplexes. Chem Asian J V. 11 1107 2016.
ISSN: ESSN 1861-471X
PubMed: 26865223
DOI: 10.1002/ASIA.201600116