Sodium 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:

Potassium	(K)	3 atoms
Fluorine	(F)	5 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T, PDB code: 8k7w:
Jump to Sodium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na105 b:47.6 occ:1.00 N7 A:G30 4.4 49.3 1.0 O6 A:G30 4.6 46.2 1.0 O4 A:U31 4.7 42.8 1.0 O6 A:G33 4.9 45.3 1.0 C5 A:G30 4.9 47.8 1.0 C6 A:G30 5.0 45.5 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na106 b:64.9 occ:1.00 O4 A:U21 2.6 53.5 1.0 O A:HOH214 3.0 51.9 1.0 C4 A:U21 3.8 52.7 1.0 N6 A:A20 4.1 51.9 1.0 C5 A:U21 4.6 51.5 1.0 N7 A:A20 4.6 52.6 1.0 N3 A:U21 4.8 51.7 1.0 C6 A:A20 5.0 51.8 1.0

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