Fluorine 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:

Magnesium	(Mg)	6 atoms
Potassium	(K)	2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the A New Fluorescent Rna Aptamer Bound with N571, PDB code: 8hzj:
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 N571


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 N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:53.2 occ:1.00 F23 A:O00107 0.0 53.2 1.0 C04 A:O00107 1.4 45.7 1.0 C03 A:O00107 2.4 44.9 1.0 C05 A:O00107 2.4 41.6 1.0 O25 A:O00107 2.7 46.5 1.0 C02 A:O00107 3.6 46.0 1.0 C06 A:O00107 3.7 41.0 1.0 O4' A:C30 4.1 46.0 1.0 C01 A:O00107 4.1 43.7 1.0 C1' A:C30 4.2 49.5 1.0 C2 A:A15 4.2 44.6 1.0 N1 A:A15 4.3 43.0 1.0 F24 A:O00107 4.7 44.1 1.0 C07 A:O00107 4.9 38.3 1.0 N1 A:C30 4.9 48.5 1.0

Fluorine binding site 2 out of 4 in the A New Fluorescent Rna Aptamer Bound with N571


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 N571 within 5.0Å range: probe atom residue distance (Å) B Occ A:F107 b:44.1 occ:1.00 F24 A:O00107 0.0 44.1 1.0 C02 A:O00107 1.4 46.0 1.0 C03 A:O00107 2.3 44.9 1.0 C01 A:O00107 2.4 43.7 1.0 O25 A:O00107 2.7 46.5 1.0 C5' A:A29 3.0 39.3 1.0 C4' A:A29 3.4 44.8 1.0 C04 A:O00107 3.6 45.7 1.0 C06 A:O00107 3.7 41.0 1.0 O2' A:G28 3.8 35.5 1.0 O4' A:C30 3.9 46.0 1.0 C05 A:O00107 4.1 41.6 1.0 O5' A:A29 4.3 39.3 1.0 O4' A:A29 4.3 42.9 1.0 C5' A:C30 4.3 52.6 1.0 C6 A:C30 4.4 45.1 1.0 C3' A:A29 4.5 43.9 1.0 O3' A:G28 4.6 40.2 1.0 N6 A:A15 4.7 41.4 1.0 F23 A:O00107 4.7 53.2 1.0 C4' A:C30 4.7 49.5 1.0 C2' A:G28 4.8 33.6 1.0 C07 A:O00107 4.9 38.3 1.0 O3' A:A29 4.9 49.2 1.0 C1' A:C30 4.9 49.5 1.0 OP1 A:C30 4.9 50.5 1.0 N11 A:O00107 5.0 37.7 1.0 N1 A:C30 5.0 48.5 1.0

Fluorine binding site 3 out of 4 in the A New Fluorescent Rna Aptamer Bound with N571


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 N571 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:40.3 occ:1.00 F23 B:O00105 0.0 40.3 1.0 C04 B:O00105 1.4 39.0 1.0 C03 B:O00105 2.4 43.7 1.0 C05 B:O00105 2.4 38.0 1.0 O25 B:O00105 2.7 44.6 1.0 C5' B:A29 3.2 35.6 1.0 C02 B:O00105 3.6 40.9 1.0 C4' B:A29 3.6 34.6 1.0 C06 B:O00105 3.6 38.4 1.0 O2' B:G28 3.7 38.0 1.0 O4' B:C30 4.0 41.5 1.0 C6 B:C30 4.1 38.3 1.0 C01 B:O00105 4.1 39.0 1.0 O B:HOH207 4.3 37.5 1.0 O5' B:C30 4.5 34.5 1.0 O5' B:A29 4.5 33.4 1.0 OP1 B:C30 4.5 38.2 1.0 O4' B:A29 4.6 31.4 1.0 C5 B:C30 4.6 34.5 1.0 O3' B:G28 4.6 36.1 1.0 F24 B:O00105 4.7 50.8 1.0 C5' B:C30 4.7 38.7 1.0 C3' B:A29 4.7 32.3 1.0 N1 B:C30 4.8 39.8 1.0 C07 B:O00105 4.8 37.3 1.0 C2' B:G28 4.8 35.3 1.0 N11 B:O00105 4.9 36.1 1.0 OP1 B:A29 4.9 35.1 1.0 N6 B:A15 4.9 38.3 1.0 C1' B:C30 4.9 39.1 1.0

Fluorine binding site 4 out of 4 in the A New Fluorescent Rna Aptamer Bound with N571


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 N571 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:50.8 occ:1.00 F24 B:O00105 0.0 50.8 1.0 C02 B:O00105 1.4 40.9 1.0 C03 B:O00105 2.3 43.7 1.0 C01 B:O00105 2.4 39.0 1.0 O25 B:O00105 2.7 44.6 1.0 C04 B:O00105 3.6 39.0 1.0 C06 B:O00105 3.7 38.4 1.0 O4' B:C30 4.1 41.5 1.0 C05 B:O00105 4.1 38.0 1.0 C1' B:C30 4.1 39.1 1.0 O B:HOH215 4.2 38.2 1.0 C2 B:A15 4.5 34.5 1.0 N1 B:A15 4.6 32.6 1.0 F23 B:O00105 4.7 40.3 1.0 N1 B:C30 4.8 39.8 1.0 C07 B:O00105 4.9 37.3 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