Potassium in PDB 8hzj: A New Fluorescent Rna Aptamer Bound with N571

The structure of A New Fluorescent Rna Aptamer Bound with N571, PDB code: 8hzj was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.37 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.316, 48.173, 58.304, 90, 116.03, 90
R / Rfree (%)	18.8 / 25.9

The structure of A New Fluorescent Rna Aptamer Bound with N571 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	6 atoms

The binding sites of Potassium atom in the A New Fluorescent Rna Aptamer Bound with N571 (pdb code 8hzj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the A New Fluorescent Rna Aptamer Bound with N571, PDB code: 8hzj:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:53.7 occ:1.00 O B:HOH211 2.8 34.8 1.0 O3' A:G20 3.3 26.5 1.0 OP1 B:U8 3.3 34.2 1.0 OP2 B:U8 3.3 33.4 1.0 N7 A:A21 3.4 27.0 1.0 P B:U8 3.7 34.2 1.0 O2' A:G20 3.8 29.6 1.0 OP1 A:A21 3.8 31.6 1.0 C8 A:A21 3.9 30.3 1.0 O3' B:U7 4.1 35.2 1.0 O2' B:U7 4.2 36.9 1.0 C3' A:G20 4.2 23.8 1.0 P A:A21 4.3 32.6 1.0 C4' A:G20 4.4 26.1 1.0 C2' B:U7 4.4 30.6 1.0 OP2 B:A27 4.5 28.6 1.0 C2' A:G20 4.6 25.5 1.0 N6 A:A22 4.6 29.3 1.0 C5 A:A21 4.6 26.1 1.0 C3' B:U7 4.8 33.2 1.0 OP1 B:A27 4.8 26.4 1.0 O B:HOH210 4.9 39.1 1.0

Potassium binding site 2 out of 2 in the A New Fluorescent Rna Aptamer Bound with N571


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of A New Fluorescent Rna Aptamer Bound with N571 within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:46.5 occ:1.00 N7 B:A21 3.0 37.1 1.0 O3' B:G20 3.1 33.3 1.0 OP1 B:A21 3.1 39.8 1.0 OP1 A:U8 3.4 32.9 1.0 C8 B:A21 3.5 35.7 1.0 O2' A:U7 3.7 37.9 1.0 P A:U8 3.8 36.4 1.0 P B:A21 3.8 41.3 1.0 OP2 A:U8 3.8 34.8 1.0 O2' B:G20 3.8 31.7 1.0 C2' A:U7 3.8 38.7 1.0 O3' A:U7 3.9 41.7 1.0 C3' B:G20 4.2 27.8 1.0 C5 B:A21 4.3 37.9 1.0 C3' A:U7 4.3 42.0 1.0 C4' B:G20 4.5 29.7 1.0 O A:HOH212 4.5 28.5 1.0 C2' B:G20 4.6 30.4 1.0 N6 B:A22 4.6 41.3 1.0 OP2 A:A27 4.6 36.6 1.0 O5' B:A21 4.7 32.2 1.0 N6 B:A21 4.8 34.6 1.0 OP1 A:A27 4.8 30.0 1.0 N9 B:A21 4.9 35.9 1.0 OP2 B:A21 5.0 30.2 1.0

K.Huang, Q.Song, M.Fang, D.Yao, X.Shen, X.Xu, X.Chen, L.Zhu, Y.Yang, A.Ren. Structural Basis of A Small Monomeric Clivia Fluorogenic Rna with A Large Stokes Shift. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38816645
DOI: 10.1038/S41589-024-01633-1