Fluorine 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
Potassium	(K)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the A New Fluorescent Rna Aptamer Bound with N565, PDB code: 8hzf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F105 b:61.5 occ:1.00 F23 A:NJL105 0.0 61.5 1.0 C04 A:NJL105 1.4 53.7 1.0 C03 A:NJL105 2.3 51.5 1.0 C05 A:NJL105 2.4 53.3 1.0 O25 A:NJL105 2.7 48.9 1.0 C5' A:A29 3.0 50.5 1.0 C4' A:A29 3.3 51.3 1.0 C02 A:NJL105 3.6 55.4 1.0 C06 A:NJL105 3.7 54.5 1.0 O4' A:C30 3.8 63.9 1.0 O5' A:C30 3.9 46.7 1.0 C6 A:C30 4.0 57.4 1.0 O2' A:G28 4.1 47.6 1.0 C01 A:NJL105 4.1 55.0 1.0 O4' A:A29 4.2 52.3 1.0 O5' A:A29 4.4 49.3 1.0 C3' A:A29 4.4 54.9 1.0 N1 A:C30 4.6 59.8 1.0 C1' A:C30 4.6 61.4 1.0 F24 A:NJL105 4.7 62.1 1.0 C5 A:C30 4.7 53.1 1.0 O3' A:G28 4.7 58.8 1.0 C5' A:C30 4.7 57.7 1.0 O3' A:A29 4.8 61.1 1.0 P A:C30 4.9 51.8 1.0 C4' A:C30 4.9 59.0 1.0 C07 A:NJL105 4.9 57.9 1.0 OP1 A:A29 5.0 57.8 1.0 N11 A:NJL105 5.0 48.5 1.0 C2' A:G28 5.0 44.3 1.0 N6 A:A15 5.0 50.5 1.0

Fluorine binding site 2 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A New Fluorescent Rna Aptamer Bound with N565 within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:62.1 occ:1.00 F24 A:NJL105 0.0 62.1 1.0 C02 A:NJL105 1.4 55.4 1.0 C03 A:NJL105 2.3 51.5 1.0 C01 A:NJL105 2.4 55.0 1.0 O25 A:NJL105 2.7 48.9 1.0 C04 A:NJL105 3.6 53.7 1.0 C06 A:NJL105 3.7 54.5 1.0 C05 A:NJL105 4.1 53.3 1.0 C1' A:C30 4.2 61.4 1.0 N1 A:A15 4.3 53.8 1.0 O4' A:C30 4.3 63.9 1.0 C2 A:A15 4.3 51.2 1.0 F23 A:NJL105 4.7 61.5 1.0 C07 A:NJL105 4.9 57.9 1.0

Fluorine binding site 3 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of A New Fluorescent Rna Aptamer Bound with N565 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:56.5 occ:1.00 F23 B:NJL105 0.0 56.5 1.0 C04 B:NJL105 1.4 48.8 1.0 C03 B:NJL105 2.3 45.1 1.0 C05 B:NJL105 2.4 48.7 1.0 O25 B:NJL105 2.8 39.1 1.0 C02 B:NJL105 3.6 44.5 1.0 C06 B:NJL105 3.7 51.8 1.0 C1' B:C30 4.1 46.8 1.0 C01 B:NJL105 4.1 49.6 1.0 O4' B:C30 4.1 36.7 1.0 C2 B:A15 4.4 55.5 1.0 N1 B:A15 4.5 61.0 1.0 F24 B:NJL105 4.7 52.1 1.0 O2 B:C30 4.8 49.9 1.0 N1 B:C30 4.8 50.9 1.0 C07 B:NJL105 4.9 55.2 1.0

Fluorine binding site 4 out of 4 in the A New Fluorescent Rna Aptamer Bound with N565


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of A New Fluorescent Rna Aptamer Bound with N565 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:52.1 occ:1.00 F24 B:NJL105 0.0 52.1 1.0 C02 B:NJL105 1.4 44.5 1.0 C03 B:NJL105 2.3 45.1 1.0 C01 B:NJL105 2.4 49.6 1.0 O25 B:NJL105 2.7 39.1 1.0 C5' B:A29 3.1 48.0 1.0 C04 B:NJL105 3.6 48.8 1.0 C4' B:A29 3.6 47.4 1.0 C06 B:NJL105 3.6 51.8 1.0 O2' B:G28 3.6 44.1 1.0 C05 B:NJL105 4.1 48.7 1.0 O3' B:G28 4.2 47.0 1.0 O4' B:C30 4.3 36.7 1.0 O5' B:A29 4.3 43.1 1.0 O4' B:A29 4.6 44.0 1.0 N6 B:A15 4.6 54.6 1.0 OP1 B:A29 4.6 48.4 1.0 C2' B:G28 4.6 46.8 1.0 C6 B:C30 4.6 47.0 1.0 OP1 B:C30 4.7 49.4 1.0 F23 B:NJL105 4.7 56.5 1.0 C3' B:A29 4.7 50.6 1.0 P B:A29 4.7 63.2 1.0 C07 B:NJL105 4.8 55.2 1.0 N11 B:NJL105 4.9 52.4 1.0 O5' B:C30 4.9 45.6 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