Fluorine in PDB 4kzd: Crystal Structure of An Rna Aptamer in Complex with Fluorophore and Fab

The structure of Crystal Structure of An Rna Aptamer in Complex with Fluorophore and Fab, PDB code: 4kzd was solved by H.Huang, N.B.Suslov, N.Li, 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)	46.69 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.425, 79.602, 95.210, 90.00, 111.65, 90.00
R / Rfree (%)	17.9 / 21.1

The structure of Crystal Structure of An Rna Aptamer in Complex with Fluorophore and Fab also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of An Rna Aptamer in Complex with Fluorophore and Fab (pdb code 4kzd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of An Rna Aptamer in Complex with Fluorophore and Fab, PDB code: 4kzd:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of An Rna Aptamer in Complex with Fluorophore and 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 in Complex with Fluorophore and Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F103 b:85.6 occ:1.00 F8 R:1TU103 0.0 85.6 1.0 C6 R:1TU103 1.3 86.1 1.0 C1 R:1TU103 2.4 84.8 1.0 C5 R:1TU103 2.5 86.1 1.0 O9 R:1TU103 2.9 87.0 1.0 C4 R:U50 3.1 88.5 1.0 O4 R:U50 3.1 85.2 1.0 C4 R:G23 3.2 84.3 1.0 O2' R:G23 3.2 85.8 1.0 N3 R:G23 3.3 84.6 1.0 C5 R:U50 3.3 85.8 1.0 N9 R:G23 3.5 82.9 1.0 N3 R:U50 3.6 89.1 1.0 C2 R:1TU103 3.6 88.7 1.0 C2 R:G23 3.8 84.0 1.0 C5 R:G23 3.8 85.4 1.0 C4 R:1TU103 3.8 85.7 1.0 C1' R:G23 3.8 80.9 1.0 C6 R:U50 4.0 90.5 1.0 C2' R:G23 4.1 81.3 1.0 C8 R:G23 4.1 83.7 1.0 C3 R:1TU103 4.2 87.4 1.0 N1 R:G23 4.2 84.0 1.0 N7 R:G23 4.3 84.0 1.0 C6 R:G23 4.3 85.8 1.0 C2 R:U50 4.3 91.4 1.0 N2 R:G23 4.5 83.5 1.0 N1 R:U50 4.5 92.9 1.0 C10 R:1TU103 4.8 90.0 1.0 F7 R:1TU103 4.9 90.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of An Rna Aptamer in Complex with Fluorophore and 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 in Complex with Fluorophore and Fab within 5.0Å range: probe atom residue distance (Å) B Occ R:F103 b:90.7 occ:1.00 F7 R:1TU103 0.0 90.7 1.0 C4 R:1TU103 1.3 85.7 1.0 C3 R:1TU103 2.4 87.4 1.0 C5 R:1TU103 2.4 86.1 1.0 O9 R:1TU103 2.8 87.0 1.0 O2' R:A53 3.3 94.9 1.0 C2' R:A53 3.4 98.2 1.0 C8 R:A53 3.5 91.9 1.0 O2 R:U50 3.5 91.5 1.0 C2 R:1TU103 3.7 88.7 1.0 C6 R:1TU103 3.8 86.1 1.0 N7 R:G23 3.9 84.0 1.0 C8 R:G23 4.0 83.7 1.0 OP2 R:A53 4.0 0.3 1.0 C2 R:U50 4.0 91.4 1.0 N9 R:A53 4.0 92.1 1.0 N7 R:A53 4.1 88.8 1.0 C1 R:1TU103 4.2 84.8 1.0 O5' R:A53 4.3 0.3 1.0 C1' R:A53 4.3 94.9 1.0 N3 R:U50 4.3 89.1 1.0 N2 R:G54 4.3 88.4 1.0 C3' R:A53 4.5 0.7 1.0 N12 R:1TU103 4.7 92.8 1.0 P R:A53 4.8 0.3 1.0 C5 R:G23 4.8 85.4 1.0 N1 R:U50 4.9 92.9 1.0 C10 R:1TU103 4.9 90.0 1.0 O2' R:G22 4.9 78.8 1.0 N9 R:G23 4.9 82.9 1.0 C4 R:A53 4.9 91.7 1.0 C5 R:A53 4.9 91.0 1.0 F8 R:1TU103 4.9 85.6 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