Fluorine in PDB 4nlf: 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl

The structure of 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl, PDB code: 4nlf was solved by E.Ennifar, R.Micura, M.Kosutic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.17 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.170, 39.570, 29.920, 90.00, 90.92, 90.00
R / Rfree (%)	9.9 / 11.6

The binding sites of Fluorine atom in the 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl (pdb code 4nlf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl, PDB code: 4nlf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:10.9 occ:0.67 F1' A:6FC2667 0.0 10.9 0.7 C7' A:6FC2667 1.3 10.7 1.0 F3' A:6FC2667 2.1 11.2 0.7 F2' A:6FC2667 2.2 11.0 0.8 S2' A:6FC2667 2.5 9.2 1.0 C2' A:6FC2667 4.0 7.6 1.0 H1'1 A:6FC2667 4.1 9.0 1.0 H2'1 A:6FC2667 4.2 9.1 1.0 O A:HOH2921 4.5 17.5 0.7 O A:HOH2871 4.6 12.8 0.7 H5' A:G2668 4.6 8.1 1.0 C1' A:6FC2667 4.6 7.5 1.0 O2 A:6FC2667 4.8 10.2 1.0

Fluorine binding site 2 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:11.0 occ:0.79 F2' A:6FC2667 0.0 11.0 0.8 C7' A:6FC2667 1.3 10.7 1.0 F3' A:6FC2667 2.2 11.2 0.7 F1' A:6FC2667 2.2 10.9 0.7 S2' A:6FC2667 2.6 9.2 1.0 H2'1 A:6FC2667 2.7 9.1 1.0 C2' A:6FC2667 3.1 7.6 1.0 O A:HOH2921 3.2 17.5 0.7 O2 A:6FC2667 3.3 10.2 1.0 H5' A:G2668 3.4 8.1 1.0 O4' A:G2668 3.5 5.9 1.0 H1'1 A:6FC2667 3.6 9.0 1.0 H4' A:G2668 3.7 7.8 1.0 C1' A:6FC2667 3.9 7.5 1.0 O A:HOH2872 3.9 14.6 0.7 C4' A:G2668 4.0 6.5 1.0 C5' A:G2668 4.1 6.8 1.0 C2 A:6FC2667 4.3 8.1 1.0 H1' A:G2668 4.4 6.7 1.0 C3' A:6FC2667 4.4 7.3 1.0 O A:HOH2947 4.4 14.9 0.6 C1' A:G2668 4.5 5.6 1.0 N1 A:6FC2667 4.5 7.4 1.0 HO2' A:G2668 4.5 9.8 1.0 O3' A:6FC2667 4.7 7.1 1.0 H5'' A:G2668 4.8 8.1 1.0 H3'1 A:6FC2667 4.9 8.7 1.0 O5' A:G2668 5.0 6.8 1.0

Fluorine binding site 3 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 2'-Trifluoromethylthio-2'-Deoxycytidine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:11.2 occ:0.74 F3' A:6FC2667 0.0 11.2 0.7 C7' A:6FC2667 1.3 10.7 1.0 F1' A:6FC2667 2.1 10.9 0.7 F2' A:6FC2667 2.2 11.0 0.8 H1'1 A:6FC2667 2.4 9.0 1.0 S2' A:6FC2667 2.6 9.2 1.0 O2 A:6FC2667 3.0 10.2 1.0 O A:HOH2911 3.1 19.3 0.8 C1' A:6FC2667 3.2 7.5 1.0 C2' A:6FC2667 3.2 7.6 1.0 H2'1 A:6FC2667 3.4 9.1 1.0 O A:HOH2871 3.4 12.8 0.7 C2 A:6FC2667 4.0 8.1 1.0 N1 A:6FC2667 4.1 7.4 1.0 O4' A:6FC2667 4.2 7.6 1.0 O A:HOH2872 4.4 14.6 0.7 C3' A:6FC2667 4.6 7.3 1.0 H4'1 A:6FC2667 4.7 8.6 1.0 C4' A:6FC2667 4.9 7.2 1.0 O4' A:G2668 5.0 5.9 1.0

E.Ennifar, R.Micura, M.Kosutic. 2'-Trifluoromethylthio-Modified Rna: Synthesis, X-Ray Structure, Thermodynamic Analysis, and Applications To Be Published.