Potassium in PDB 8hzf: A New Fluorescent Rna Aptamer Bound with N565

The structure of A New Fluorescent Rna Aptamer Bound with N565, PDB code: 8hzf 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)	40.20 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.634, 47.237, 56.17, 90, 115.26, 90
R / Rfree (%)	18.2 / 25.6

The structure of A New Fluorescent Rna Aptamer Bound with N565 also contains other interesting chemical elements:

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

The binding sites of Potassium atom in the A New Fluorescent Rna Aptamer Bound with N565 (pdb code 8hzf). 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 N565, PDB code: 8hzf:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:67.8 occ:1.00 O3' A:G20 2.7 56.1 1.0 O2' A:G20 2.8 42.5 1.0 N7 A:A21 3.0 48.2 1.0 OP1 B:U8 3.3 56.5 1.0 OP1 A:A21 3.4 51.3 1.0 C3' A:G20 3.5 49.2 1.0 C8 A:A21 3.6 43.4 1.0 C2' A:G20 3.7 45.6 1.0 C4' A:G20 3.7 48.6 1.0 P A:A21 3.8 58.3 1.0 N6 A:A22 3.9 46.9 1.0 C5 A:A21 4.1 48.3 1.0 P B:U8 4.2 53.1 1.0 O3' B:U7 4.3 53.2 1.0 OP2 B:U8 4.4 50.1 1.0 O5' A:A21 4.5 50.1 1.0 N7 A:A22 4.5 48.2 1.0 OP1 B:C26 4.5 44.1 1.0 C2' B:U7 4.6 53.8 1.0 C6 A:A22 4.6 42.4 1.0 O2' B:U7 4.6 59.2 1.0 N6 A:A21 4.6 45.2 1.0 O4' A:G20 4.7 45.4 1.0 C1' A:G20 4.7 44.4 1.0 C5' A:G20 4.8 49.8 1.0 OP2 B:A27 4.8 50.9 1.0 C5 A:A22 4.8 46.5 1.0 C6 A:A21 4.8 50.0 1.0 N9 A:A21 4.9 44.0 1.0 C3' B:U7 4.9 47.4 1.0 OP1 B:A27 4.9 50.0 1.0

Potassium binding site 2 out of 2 in the A New Fluorescent Rna Aptamer Bound with N565


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 N565 within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:50.6 occ:1.00 N7 B:A21 2.7 44.9 1.0 OP1 A:U8 2.9 54.8 1.0 O3' B:G20 3.0 50.6 1.0 O2' B:G20 3.3 46.4 1.0 C8 B:A21 3.5 46.4 1.0 P A:U8 3.6 42.0 1.0 OP1 B:A21 3.7 54.3 1.0 N6 B:A22 3.8 51.1 1.0 C5 B:A21 3.8 50.3 1.0 O3' A:U7 3.9 54.3 1.0 C3' B:G20 3.9 46.6 1.0 OP2 A:U8 3.9 39.7 1.0 P B:A21 4.0 52.3 1.0 O2' A:U7 4.1 58.8 1.0 N6 B:A21 4.1 52.8 1.0 C2' A:U7 4.2 53.3 1.0 C2' B:G20 4.2 44.3 1.0 C4' B:G20 4.2 41.7 1.0 C6 B:A21 4.4 54.9 1.0 C3' A:U7 4.5 50.1 1.0 C6 B:A22 4.6 53.5 1.0 O5' B:A21 4.7 46.4 1.0 N9 B:A21 4.8 47.2 1.0 N7 B:A22 4.8 55.0 1.0 OP1 A:C26 4.9 46.1 1.0 OP2 A:A27 4.9 40.2 1.0 C4 B:A21 4.9 46.8 1.0 C5 B:A22 5.0 52.8 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