Potassium in PDB 8hzm: A New Fluorescent Rna Aptamer Bound with N, Manganese Soak

The structure of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak, PDB code: 8hzm 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)	39.14 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.694, 46.871, 56.722, 90, 113.7, 90
R / Rfree (%)	20.5 / 25.7

The structure of A New Fluorescent Rna Aptamer Bound with N, Manganese Soak also contains other interesting chemical elements:

Manganese	(Mn)	11 atoms
Magnesium	(Mg)	5 atoms

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

Potassium binding site 1 out of 2 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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 N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:K108 b:61.8 occ:1.00 O A:HOH210 2.6 49.5 1.0 OP2 A:U8 2.8 71.5 1.0 OP1 A:U8 2.9 57.1 1.0 N7 B:A21 3.0 64.0 1.0 P A:U8 3.2 67.7 1.0 OP1 B:A21 3.2 54.1 1.0 O3' B:G20 3.3 53.3 1.0 O B:HOH206 3.4 53.4 1.0 C8 B:A21 3.5 66.9 1.0 O2' A:U7 3.8 63.4 1.0 O3' A:U7 3.9 59.2 1.0 P B:A21 3.9 53.0 1.0 C2' A:U7 4.1 67.2 1.0 O2' B:G20 4.1 52.2 1.0 C5 B:A21 4.2 64.2 1.0 OP1 A:A27 4.3 68.6 1.0 N6 B:A22 4.4 59.4 1.0 C3' B:G20 4.4 51.7 1.0 C3' A:U7 4.5 58.4 1.0 OP2 A:A27 4.5 64.8 1.0 O5' A:U8 4.7 60.5 1.0 N6 B:A21 4.8 70.7 1.0 N9 B:A21 4.8 61.9 1.0 C2' B:G20 4.9 56.3 1.0 C4' B:G20 4.9 54.9 1.0 O5' B:A21 4.9 49.5 1.0 P A:A27 5.0 58.2 1.0 C6 B:A21 5.0 70.1 1.0 OP2 B:A21 5.0 60.5 1.0

Potassium binding site 2 out of 2 in the A New Fluorescent Rna Aptamer Bound with N, Manganese Soak


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 N, Manganese Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:K109 b:70.5 occ:1.00 O B:HOH216 2.6 51.3 1.0 N7 A:A21 2.7 51.7 1.0 OP1 B:U8 3.1 61.5 1.0 OP2 B:U8 3.1 58.4 1.0 C8 A:A21 3.4 53.1 1.0 O3' A:G20 3.4 47.5 1.0 P B:U8 3.5 56.0 1.0 O2' A:G20 3.6 49.7 1.0 OP1 A:A21 3.8 47.8 1.0 O2' B:U7 3.9 63.5 1.0 C5 A:A21 3.9 53.5 1.0 C2' B:U7 4.1 59.2 1.0 N6 A:A22 4.1 46.1 1.0 N6 A:A21 4.2 52.0 1.0 O3' B:U7 4.3 52.9 1.0 P A:A21 4.3 44.8 1.0 C3' A:G20 4.4 41.2 1.0 C6 A:A21 4.5 51.9 1.0 C2' A:G20 4.6 39.4 1.0 C4' A:G20 4.7 45.0 1.0 N9 A:A21 4.7 52.4 1.0 C3' B:U7 4.7 59.7 1.0 C6 A:A22 4.9 50.0 1.0 C4 A:A21 5.0 52.3 1.0 O5' B:U8 5.0 48.8 1.0 OP2 B:A27 5.0 48.3 1.0 O5' A:A21 5.0 45.4 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