Fluorine in PDB 4q9r: Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab

The structure of Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab, PDB code: 4q9r was solved by H.Huang, N.B.Suslov, N.-S.Li, S.A.Shelke, M.E.Evans, Y.Koldobskaya, P.A.Rice, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.68 / 3.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.515, 78.986, 94.357, 90.00, 112.42, 90.00
R / Rfree (%)	20.3 / 25.3

The structure of Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab (pdb code 4q9r). 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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab, PDB code: 4q9r:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab


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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F102 b:0.1 occ:1.00 F8 R:2ZY102 0.0 0.1 1.0 C6 R:2ZY102 1.3 0.1 1.0 C1 R:2ZY102 2.4 0.3 1.0 C5 R:2ZY102 2.4 1.0 1.0 O9 R:2ZY102 2.9 0.8 1.0 O4 R:U50 3.0 0.4 1.0 C4 R:U50 3.0 0.2 1.0 O2' R:G23 3.3 0.3 1.0 N3 R:U50 3.4 0.3 1.0 N3 R:G23 3.4 0.4 1.0 C5 R:U50 3.5 0.9 1.0 C4 R:G23 3.5 0.6 1.0 C2 R:2ZY102 3.6 0.4 1.0 C4 R:2ZY102 3.8 0.5 1.0 C2 R:G23 3.8 0.9 1.0 N9 R:G23 3.9 0.3 1.0 C5 R:G23 4.0 0.4 1.0 C3 R:2ZY102 4.1 0.8 1.0 C2 R:U50 4.1 0.5 1.0 C6 R:U50 4.2 0.1 1.0 C1' R:G23 4.2 1.0 1.0 C2' R:G23 4.3 0.6 1.0 N1 R:G23 4.3 0.7 1.0 N2 R:G23 4.4 1.0 1.0 C6 R:G23 4.5 0.8 1.0 N1 R:U50 4.5 0.6 1.0 C8 R:G23 4.5 0.3 1.0 N7 R:G23 4.6 0.9 1.0 C10 R:2ZY102 4.9 0.8 1.0 F7 R:2ZY102 4.9 0.1 1.0 N7 R:A53 4.9 0.2 1.0 O2 R:U50 4.9 0.2 1.0

Fluorine binding site 2 out of 5 in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab


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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F102 b:0.1 occ:1.00 F7 R:2ZY102 0.0 0.1 1.0 C4 R:2ZY102 1.3 0.5 1.0 C3 R:2ZY102 2.3 0.8 1.0 C5 R:2ZY102 2.5 1.0 1.0 O9 R:2ZY102 2.9 0.8 1.0 O2 R:U50 3.5 0.2 1.0 C2 R:2ZY102 3.6 0.4 1.0 N7 R:G23 3.6 0.9 1.0 C8 R:G23 3.7 0.3 1.0 C8 R:A53 3.7 0.1 1.0 O2' R:A53 3.8 0.9 1.0 C6 R:2ZY102 3.8 0.1 1.0 C2' R:A53 3.8 0.8 1.0 OP2 R:A53 4.0 0.9 1.0 N2 R:G54 4.0 0.2 1.0 C2 R:U50 4.1 0.5 1.0 O2' R:G22 4.2 0.5 1.0 N7 R:A53 4.2 0.2 1.0 C1 R:2ZY102 4.2 0.3 1.0 N9 R:A53 4.3 0.4 1.0 C5 R:G23 4.5 0.4 1.0 N3 R:U50 4.5 0.3 1.0 C10 R:2ZY102 4.5 0.8 1.0 O5' R:A53 4.5 0.8 1.0 N9 R:G23 4.6 0.3 1.0 C1' R:A53 4.7 0.8 1.0 P R:A53 4.9 0.7 1.0 F8 R:2ZY102 4.9 0.1 1.0

Fluorine binding site 3 out of 5 in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab


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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F102 b:0.5 occ:1.00 F20 R:2ZY102 0.0 0.5 1.0 C19 R:2ZY102 1.3 0.0 1.0 F21 R:2ZY102 2.2 0.5 1.0 F22 R:2ZY102 2.2 0.4 1.0 C16 R:2ZY102 2.2 0.4 1.0 N14 R:2ZY102 3.5 0.4 1.0 O2 R:U29 3.6 1.0 1.0 N2 R:G28 4.1 0.9 1.0 O18 R:2ZY102 4.3 0.2 1.0 C15 R:2ZY102 4.3 0.1 1.0 O2' R:A58 4.4 0.9 1.0 C13 R:2ZY102 4.5 0.6 1.0 C17 R:2ZY102 4.5 0.9 1.0 N3 R:A58 4.5 0.7 1.0 C2 R:A58 4.7 0.5 1.0 O2' R:U29 4.7 0.1 1.0 C2 R:U29 4.8 0.8 1.0 C2 R:A53 4.8 0.2 1.0 O4' R:C30 4.9 0.2 1.0

Fluorine binding site 4 out of 5 in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab


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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F102 b:0.5 occ:1.00 F21 R:2ZY102 0.0 0.5 1.0 C19 R:2ZY102 1.3 0.0 1.0 F20 R:2ZY102 2.2 0.5 1.0 F22 R:2ZY102 2.2 0.4 1.0 C16 R:2ZY102 2.2 0.4 1.0 N3 R:A58 2.8 0.7 1.0 C2 R:A58 3.1 0.5 1.0 C17 R:2ZY102 3.1 0.9 1.0 O2' R:A58 3.2 0.9 1.0 N14 R:2ZY102 3.2 0.4 1.0 C4 R:A58 3.6 0.4 1.0 C13 R:2ZY102 3.8 0.6 1.0 N1 R:A58 4.0 0.6 1.0 C2' R:A58 4.3 0.7 1.0 N9 R:A58 4.3 0.7 1.0 C1' R:A58 4.5 0.4 1.0 C5 R:A58 4.5 0.9 1.0 C15 R:2ZY102 4.5 0.1 1.0 C6 R:A58 4.7 0.2 1.0 N2 R:G59 4.7 0.0 1.0 N7 R:G54 4.8 0.5 1.0 O18 R:2ZY102 5.0 0.2 1.0

Fluorine binding site 5 out of 5 in the Crystal Structure of An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab


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 An Rna Aptamer Bound to Trifluoroethyl-Ligand Analog in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F102 b:0.4 occ:1.00 F22 R:2ZY102 0.0 0.4 1.0 C19 R:2ZY102 1.3 0.0 1.0 F21 R:2ZY102 2.2 0.5 1.0 F20 R:2ZY102 2.2 0.5 1.0 C16 R:2ZY102 2.2 0.4 1.0 N14 R:2ZY102 2.5 0.4 1.0 C17 R:2ZY102 2.9 0.9 1.0 C13 R:2ZY102 3.0 0.6 1.0 C15 R:2ZY102 3.5 0.1 1.0 C2 R:A53 3.7 0.2 1.0 C2 R:A58 3.7 0.5 1.0 N3 R:A53 3.7 0.3 1.0 O18 R:2ZY102 4.0 0.2 1.0 N12 R:2ZY102 4.1 0.5 1.0 N3 R:A58 4.1 0.7 1.0 N1 R:A58 4.3 0.6 1.0 O2 R:U29 4.4 1.0 1.0 C11 R:2ZY102 4.4 0.7 1.0 N1 R:A53 4.8 0.9 1.0 C4 R:A53 5.0 0.2 1.0

H.Huang, N.B.Suslov, N.S.Li, S.A.Shelke, M.E.Evans, Y.Koldobskaya, P.A.Rice, J.A.Piccirilli. A G-Quadruplex-Containing Rna Activates Fluorescence in A Gfp-Like Fluorophore. Nat.Chem.Biol. V. 10 686 2014.
ISSN: ISSN 1552-4450
PubMed: 24952597
DOI: 10.1038/NCHEMBIO.1561