Potassium in PDB 8k7w: Crystal Structure of Broccoli Aptamer with Dfhbi-1T

The structure of Crystal Structure of Broccoli Aptamer with Dfhbi-1T, PDB code: 8k7w was solved by X.Peng, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.78 / 2.24
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.301, 35.006, 51.372, 90, 90, 90
R / Rfree (%)	23.6 / 27.8

The structure of Crystal Structure of Broccoli Aptamer with Dfhbi-1T also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Fluorine	(F)	5 atoms

The binding sites of Potassium atom in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T (pdb code 8k7w). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T, PDB code: 8k7w:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:49.7 occ:1.00 O4 A:U48 2.8 49.2 1.0 C4 A:U48 3.8 51.8 1.0 C5 A:U48 4.3 51.7 1.0 OP2 A:C47 4.4 48.4 1.0 C5 A:C47 4.6 46.9 1.0 N4 A:C49 4.7 54.8 1.0 OP2 A:G46 4.9 45.9 1.0 N4 A:C47 4.9 46.3 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:39.3 occ:1.00 O6 A:G11 2.4 40.6 1.0 O6 A:G38 2.5 40.2 1.0 O6 A:G40 2.8 41.0 1.0 O6 A:G6 2.8 39.9 1.0 O6 A:G7 2.9 40.3 1.0 O6 A:G10 2.9 39.7 1.0 O6 A:G35 3.0 42.5 1.0 O6 A:G42 3.0 40.7 1.0 C6 A:G11 3.3 40.8 1.0 C6 A:G38 3.4 42.3 1.0 C6 A:G6 3.5 40.1 1.0 N1 A:G11 3.6 41.7 1.0 K A:K104 3.6 42.6 1.0 N1 A:G38 3.6 42.2 1.0 C6 A:G7 3.7 39.3 1.0 C6 A:G40 3.7 43.1 1.0 N1 A:G6 3.8 37.9 1.0 C6 A:G35 3.8 42.8 1.0 N1 A:G7 3.8 39.3 1.0 C6 A:G10 3.9 39.9 1.0 C6 A:G42 3.9 41.5 1.0 N1 A:G35 4.0 41.0 1.0 N1 A:G42 4.1 42.6 1.0 N1 A:G40 4.1 43.9 1.0 N1 A:G10 4.3 40.2 1.0 C5 A:G11 4.5 40.2 1.0 C5 A:G6 4.6 39.8 1.0 C5 A:G38 4.7 42.8 1.0 C2 A:G11 4.8 41.1 1.0 C5 A:G40 4.9 44.5 1.0 C2 A:G38 4.9 42.1 1.0 C5 A:G7 4.9 38.9 1.0 C2 A:G6 5.0 39.0 1.0 N1 A:G12 5.0 41.7 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:42.6 occ:1.00 O6 A:G44 2.7 41.4 1.0 O2 A:U43 2.8 42.8 1.0 O6 A:G6 2.8 39.9 1.0 O2' A:U43 2.9 44.2 1.0 O6 A:G38 2.9 40.2 1.0 O6 A:G42 3.0 40.7 1.0 O6 A:G10 3.2 39.7 1.0 N7 A:G44 3.4 43.4 1.0 C6 A:G44 3.5 41.5 1.0 C6 A:G42 3.5 41.5 1.0 K A:K103 3.6 39.3 1.0 C6 A:G38 3.7 42.3 1.0 C5 A:G44 3.7 42.7 1.0 N1 A:G42 3.8 42.6 1.0 C6 A:G6 3.8 40.1 1.0 C2' A:U43 3.8 44.4 1.0 C6 A:G10 3.9 39.9 1.0 N1 A:G10 3.9 40.2 1.0 N1 A:G38 4.0 42.2 1.0 C2 A:U43 4.0 42.8 1.0 N1 A:G6 4.1 37.9 1.0 C1' A:U43 4.2 42.7 1.0 N4 A:C9 4.4 39.8 1.0 C5 A:G42 4.5 43.1 1.0 C8 A:G44 4.6 43.5 1.0 N1 A:U43 4.7 41.9 1.0 N1 A:G44 4.7 41.2 1.0 C2 A:G42 4.8 44.1 1.0 C5 A:G38 4.8 42.8 1.0 N3 A:U36 5.0 40.3 1.0

X.Peng, L.Huang. Structural Analysis of Various Broccoli Aptamers with Different Fluorophores To Be Published.