Fluorine in PDB 4ts2: Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions

The structure of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions, PDB code: 4ts2 was solved by K.D.Warner, M.C.Chen, W.Song, R.L.Strack, A.Thorn, S.R.Jaffrey, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.877, 49.399, 188.410, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.7

The structure of Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	3 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions (pdb code 4ts2). 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 the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions, PDB code: 4ts2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions


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 the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ Y:F104 b:91.7 occ:1.00 F1 Y:38E104 0.0 91.7 1.0 C2 Y:38E104 1.4 71.7 1.0 C3 Y:38E104 2.4 68.0 1.0 C1 Y:38E104 2.5 72.0 1.0 O1 Y:38E104 2.8 90.9 1.0 O Y:HOH202 3.0 93.1 1.0 O2 Y:U61 3.1 0.9 1.0 MG X:MG101 3.1 0.5 1.0 C8 Y:A64 3.3 83.6 1.0 C2 Y:U61 3.6 99.8 1.0 C4 Y:38E104 3.7 74.3 1.0 N7 Y:A64 3.7 85.5 1.0 C Y:38E104 3.8 74.3 1.0 N3 Y:U61 3.8 95.4 1.0 C2' Y:A64 3.9 75.3 1.0 O2' Y:A64 3.9 80.6 1.0 N9 Y:A64 4.2 77.6 1.0 C5 Y:38E104 4.2 73.2 1.0 OP2 Y:A64 4.3 90.2 1.0 C8 X:G26 4.3 78.2 1.0 N7 X:G26 4.5 74.3 1.0 N2 Y:G65 4.5 79.7 1.0 O5' Y:A64 4.6 89.4 1.0 C1' Y:A64 4.7 75.0 1.0 N1 Y:U61 4.7 0.1 1.0 C5 Y:A64 4.7 77.0 1.0 O2' X:G25 4.8 94.9 1.0 O Y:HOH203 4.8 0.9 1.0 C4 Y:U61 4.9 94.9 1.0 C4 Y:A64 5.0 74.2 1.0 F Y:38E104 5.0 0.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions


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 the Spinach Rna Aptamer in Complex with Dfhbi, Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ Y:F104 b:0.9 occ:1.00 F Y:38E104 0.0 0.9 1.0 C Y:38E104 1.4 74.3 1.0 C5 Y:38E104 2.4 73.2 1.0 C1 Y:38E104 2.5 72.0 1.0 O2' X:G26 2.9 90.5 1.0 O1 Y:38E104 3.0 90.9 1.0 C4 X:G26 3.0 73.8 1.0 N3 X:G26 3.1 73.8 1.0 N9 X:G26 3.3 77.4 1.0 O4 Y:U61 3.4 88.0 1.0 C5 X:G26 3.5 74.0 1.0 C4 Y:U61 3.6 94.9 1.0 C2 X:G26 3.6 76.8 1.0 C4 Y:38E104 3.7 74.3 1.0 C2' X:G26 3.7 81.6 1.0 C1' X:G26 3.7 80.1 1.0 C2 Y:38E104 3.8 71.7 1.0 C8 X:G26 3.9 78.2 1.0 N1 X:G26 4.0 75.7 1.0 N3 Y:U61 4.0 95.4 1.0 C5 Y:U61 4.1 96.6 1.0 N7 X:G26 4.1 74.3 1.0 C6 X:G26 4.1 74.8 1.0 C3 Y:38E104 4.2 68.0 1.0 N2 X:G26 4.4 82.0 1.0 C6 Y:U61 4.8 0.3 1.0 C6 Y:38E104 4.8 66.8 1.0 C2 Y:U61 4.9 99.8 1.0 O6 X:G31 4.9 70.0 1.0 F1 Y:38E104 5.0 91.7 1.0

K.D.Warner, M.C.Chen, W.Song, R.L.Strack, A.Thorn, S.R.Jaffrey, A.R.Ferre-D'amare. Structural Basis For Activity of Highly Efficient Rna Mimics of Green Fluorescent Protein. Nat.Struct.Mol.Biol. V. 21 658 2014.
ISSN: ESSN 1545-9985
PubMed: 25026079
DOI: 10.1038/NSMB.2865