Fluorine in PDB 8hzd: A New Fluorescent Rna Aptamer Bound with N618

The structure of A New Fluorescent Rna Aptamer Bound with N618, PDB code: 8hzd was solved by Q.Q.Song, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.16 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.494, 46.461, 56.251, 90, 113.81, 90
R / Rfree (%)	21.1 / 25.9

The structure of A New Fluorescent Rna Aptamer Bound with N618 also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Fluorine atom in the A New Fluorescent Rna Aptamer Bound with N618 (pdb code 8hzd). 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 N618, PDB code: 8hzd:
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 N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:61.6 occ:1.00 F16 A:O2I104 0.0 61.6 1.0 C14 A:O2I104 1.4 58.8 1.0 C12 A:O2I104 2.4 59.2 1.0 C15 A:O2I104 2.4 56.4 1.0 O18 A:O2I104 2.9 53.8 1.0 C13 A:O2I104 3.6 52.8 1.0 C10 A:O2I104 3.6 54.1 1.0 C1' A:C30 3.8 56.8 1.0 O4' A:C30 4.0 57.9 1.0 C11 A:O2I104 4.1 51.5 1.0 N1 A:C30 4.5 56.0 1.0 C2 A:A15 4.5 55.5 1.0 O2 A:C30 4.5 60.0 1.0 N1 A:A15 4.6 56.9 1.0 F17 A:O2I104 4.7 53.7 1.0 C2 A:C30 4.8 59.0 1.0 C09 A:O2I104 4.8 52.7 1.0 O2' A:C30 4.9 59.6 1.0

Fluorine binding site 2 out of 4 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:53.7 occ:1.00 F17 A:O2I104 0.0 53.7 1.0 C13 A:O2I104 1.4 52.8 1.0 C15 A:O2I104 2.3 56.4 1.0 C11 A:O2I104 2.4 51.5 1.0 O18 A:O2I104 2.7 53.8 1.0 C5' A:A29 3.2 49.6 1.0 C4' A:A29 3.6 49.1 1.0 C14 A:O2I104 3.6 58.8 1.0 C10 A:O2I104 3.7 54.1 1.0 O2' A:G28 3.7 48.2 1.0 O4' A:C30 4.1 57.9 1.0 C12 A:O2I104 4.1 59.2 1.0 C6 A:C30 4.3 52.6 1.0 OP1 A:C30 4.4 59.7 1.0 O5' A:A29 4.5 51.0 1.0 O4' A:A29 4.5 44.1 1.0 N6 A:A15 4.7 53.0 1.0 O5' A:C30 4.7 60.3 1.0 C3' A:A29 4.7 52.7 1.0 F16 A:O2I104 4.7 61.6 1.0 O3' A:G28 4.8 47.7 1.0 N1 A:C30 4.8 56.0 1.0 C5 A:C30 4.8 51.0 1.0 C2' A:G28 4.8 45.8 1.0 C5' A:C30 4.9 61.3 1.0 C09 A:O2I104 4.9 52.7 1.0 C1' A:C30 4.9 56.8 1.0 OP1 A:A29 5.0 60.3 1.0

Fluorine binding site 3 out of 4 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:31.9 occ:1.00 F16 B:O2I105 0.0 31.9 1.0 C14 B:O2I105 1.4 32.0 1.0 C15 B:O2I105 2.3 30.6 1.0 C12 B:O2I105 2.4 29.1 1.0 O18 B:O2I105 2.7 33.5 1.0 O B:HOH222 3.1 34.0 1.0 C5' B:A29 3.2 30.4 1.0 O2' B:G28 3.5 31.5 1.0 C13 B:O2I105 3.6 34.2 1.0 C10 B:O2I105 3.7 33.6 1.0 C4' B:A29 3.9 28.7 1.0 C11 B:O2I105 4.1 35.1 1.0 O4' B:C30 4.3 31.3 1.0 N1 B:A15 4.5 31.8 1.0 O5' B:A29 4.5 25.9 1.0 O3' B:G28 4.5 28.6 1.0 C6 B:C30 4.5 31.4 1.0 F17 B:O2I105 4.7 34.4 1.0 C2' B:G28 4.7 31.9 1.0 O4' B:A29 4.7 26.9 1.0 N6 B:A15 4.9 31.8 1.0 C09 B:O2I105 4.9 33.3 1.0 N05 B:O2I105 5.0 28.4 1.0 O5' B:C30 5.0 28.7 1.0

Fluorine binding site 4 out of 4 in the A New Fluorescent Rna Aptamer Bound with N618


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 N618 within 5.0Å range: probe atom residue distance (Å) B Occ B:F105 b:34.4 occ:1.00 F17 B:O2I105 0.0 34.4 1.0 C13 B:O2I105 1.4 34.2 1.0 C15 B:O2I105 2.3 30.6 1.0 C11 B:O2I105 2.4 35.1 1.0 O18 B:O2I105 2.7 33.5 1.0 C14 B:O2I105 3.6 32.0 1.0 C10 B:O2I105 3.7 33.6 1.0 C1' B:C30 3.8 26.2 1.0 O B:HOH238 3.8 34.0 1.0 O4' B:C30 4.0 31.3 1.0 C12 B:O2I105 4.1 29.1 1.0 N1 B:C30 4.5 29.1 1.0 O2' B:C30 4.6 28.8 1.0 F16 B:O2I105 4.7 31.9 1.0 C2 B:A15 4.7 34.4 1.0 O2 B:C30 4.7 32.8 1.0 C2' B:C30 4.8 31.4 1.0 C09 B:O2I105 4.8 33.3 1.0 C2 B:C30 4.9 30.4 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