Fluorine in PDB 8k7w: Crystal Structure of Broccoli Aptamer with Dfhbi-1T

The structure of Crystal Structure of Broccoli Aptamer with Dfhbi-1T, PDB code: 8k7w was solved by X.Peng, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.78 / 2.24
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.301, 35.006, 51.372, 90, 90, 90
R / Rfree (%)	23.6 / 27.8

The structure of Crystal Structure of Broccoli Aptamer with Dfhbi-1T also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T (pdb code 8k7w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T, PDB code: 8k7w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:43.1 occ:1.00 F8 A:2ZY101 0.0 43.1 1.0 C6 A:2ZY101 1.3 42.5 1.0 C5 A:2ZY101 2.3 42.2 1.0 C1 A:2ZY101 2.4 42.1 1.0 O9 A:2ZY101 2.6 43.3 1.0 O A:HOH210 3.1 47.1 1.0 O A:HOH211 3.3 42.9 1.0 C4 A:2ZY101 3.6 41.7 1.0 C2 A:2ZY101 3.6 41.8 1.0 O2' A:A34 3.7 43.5 1.0 C8 A:A34 3.7 43.9 1.0 C2' A:A34 3.8 44.8 1.0 C8 A:G7 3.9 40.7 1.0 N7 A:G7 3.9 40.0 1.0 N2 A:G35 4.0 41.8 1.0 O2 A:U31 4.1 47.9 1.0 C3 A:2ZY101 4.1 41.3 1.0 O A:HOH205 4.1 38.9 1.0 N7 A:A34 4.1 44.2 1.0 N9 A:A34 4.2 42.9 1.0 OP2 A:A34 4.4 51.7 1.0 O2' A:G6 4.5 41.2 1.0 C2 A:U31 4.5 47.2 1.0 C1' A:A34 4.6 43.8 1.0 F7 A:2ZY101 4.6 41.1 1.0 N3 A:U31 4.6 44.2 1.0 C10 A:2ZY101 4.8 41.9 1.0 N12 A:2ZY101 4.8 43.1 1.0 N9 A:G7 4.8 40.4 1.0 O5' A:A34 4.8 48.5 1.0 C5 A:G7 4.8 38.9 1.0 C5 A:A34 4.9 43.8 1.0 C2 A:G35 4.9 41.6 1.0 C4 A:A34 5.0 43.5 1.0 C3' A:A34 5.0 45.2 1.0

Fluorine binding site 2 out of 5 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:41.1 occ:1.00 F7 A:2ZY101 0.0 41.1 1.0 C4 A:2ZY101 1.3 41.7 1.0 C5 A:2ZY101 2.3 42.2 1.0 C3 A:2ZY101 2.4 41.3 1.0 O9 A:2ZY101 2.7 43.3 1.0 C4 A:U31 3.1 43.5 1.0 O4 A:U31 3.1 42.8 1.0 O2' A:G7 3.1 42.5 1.0 C4 A:G7 3.3 40.0 1.0 N3 A:G7 3.4 40.4 1.0 N3 A:U31 3.5 44.2 1.0 C6 A:2ZY101 3.6 42.5 1.0 C5 A:U31 3.6 45.3 1.0 N9 A:G7 3.6 40.4 1.0 C2 A:2ZY101 3.6 41.8 1.0 C5 A:G7 3.8 38.9 1.0 C2 A:G7 3.9 40.0 1.0 C2' A:G7 4.0 42.0 1.0 C1' A:G7 4.1 40.5 1.0 C1 A:2ZY101 4.1 42.1 1.0 C8 A:G7 4.1 40.7 1.0 C2 A:U31 4.2 47.2 1.0 C6 A:U31 4.2 47.1 1.0 N1 A:G7 4.3 39.3 1.0 N7 A:G7 4.3 40.0 1.0 C6 A:G7 4.3 39.3 1.0 N1 A:U31 4.5 49.1 1.0 N2 A:G7 4.6 39.0 1.0 N6 A:A34 4.6 41.2 1.0 F8 A:2ZY101 4.6 43.1 1.0 N7 A:A34 4.6 44.2 1.0 C10 A:2ZY101 4.9 41.9 1.0 O2 A:U31 5.0 47.9 1.0

Fluorine binding site 3 out of 5 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:42.3 occ:1.00 F20 A:2ZY101 0.0 42.3 1.0 C19 A:2ZY101 1.3 45.0 1.0 F21 A:2ZY101 2.1 46.9 1.0 F22 A:2ZY101 2.2 45.8 1.0 C16 A:2ZY101 2.4 43.4 1.0 N3 A:A39 3.2 46.6 1.0 C2 A:A39 3.5 47.2 1.0 N14 A:2ZY101 3.6 43.4 1.0 C4 A:A39 3.9 45.6 1.0 O2' A:A39 3.9 49.0 1.0 N1 A:A39 4.3 46.7 1.0 N9 A:A39 4.5 47.3 1.0 C15 A:2ZY101 4.5 43.8 1.0 C13 A:2ZY101 4.5 43.7 1.0 O18 A:2ZY101 4.6 43.1 1.0 C17 A:2ZY101 4.6 43.0 1.0 C5 A:A39 4.6 45.5 1.0 C1' A:A39 4.6 47.4 1.0 N2 A:G40 4.8 44.4 1.0 C6 A:A39 4.8 46.2 1.0 C2' A:A39 4.9 47.6 1.0

Fluorine binding site 4 out of 5 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:46.9 occ:1.00 F21 A:2ZY101 0.0 46.9 1.0 C19 A:2ZY101 1.3 45.0 1.0 F20 A:2ZY101 2.1 42.3 1.0 F22 A:2ZY101 2.2 45.8 1.0 C16 A:2ZY101 2.4 43.4 1.0 N14 A:2ZY101 2.8 43.4 1.0 C17 A:2ZY101 3.1 43.0 1.0 C13 A:2ZY101 3.2 43.7 1.0 C2 A:A39 3.2 47.2 1.0 N1 A:A39 3.4 46.7 1.0 N3 A:A34 3.6 43.6 1.0 N3 A:A39 3.7 46.6 1.0 C15 A:2ZY101 3.8 43.8 1.0 C2 A:A34 3.9 43.5 1.0 C6 A:A39 4.0 46.2 1.0 N12 A:2ZY101 4.2 43.1 1.0 C4 A:A39 4.3 45.6 1.0 O18 A:2ZY101 4.4 43.1 1.0 C5 A:A39 4.4 45.5 1.0 C11 A:2ZY101 4.6 42.3 1.0 N6 A:A39 4.8 45.0 1.0 C4 A:A34 4.9 43.5 1.0

Fluorine binding site 5 out of 5 in the Crystal Structure of Broccoli Aptamer with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Broccoli Aptamer with Dfhbi-1T within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:45.8 occ:1.00 F22 A:2ZY101 0.0 45.8 1.0 C19 A:2ZY101 1.3 45.0 1.0 F21 A:2ZY101 2.2 46.9 1.0 F20 A:2ZY101 2.2 42.3 1.0 C16 A:2ZY101 2.3 43.4 1.0 N14 A:2ZY101 2.8 43.4 1.0 O18 A:2ZY101 3.0 43.1 1.0 C15 A:2ZY101 3.1 43.8 1.0 C2 A:A34 3.3 43.5 1.0 O2 A:U13 3.3 44.8 1.0 N3 A:A34 3.7 43.6 1.0 C13 A:2ZY101 3.8 43.7 1.0 C11 A:2ZY101 4.2 42.3 1.0 N1 A:A34 4.3 42.7 1.0 N2 A:G12 4.3 42.1 1.0 C2 A:U13 4.5 44.7 1.0 C17 A:2ZY101 4.5 43.0 1.0 N12 A:2ZY101 4.5 43.1 1.0 C1' A:C14 4.8 47.3 1.0

X.Peng, L.Huang. Structural Analysis of Various Broccoli Aptamers with Different Fluorophores To Be Published.