Fluorine in PDB 4nmg: 2'-Trifluoromethylthio-2'-Deoxyuridine-Modified Srl

The structure of 2'-Trifluoromethylthio-2'-Deoxyuridine-Modified Srl, PDB code: 4nmg 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)	29.57 / 1.01
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	29.572, 29.572, 76.520, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 14.1

The binding sites of Fluorine atom in the 2'-Trifluoromethylthio-2'-Deoxyuridine-Modified Srl (pdb code 4nmg). 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'-Deoxyuridine-Modified Srl, PDB code: 4nmg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxyuridine-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'-Deoxyuridine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2656 b:20.2 occ:1.00 F1' A:6FU2656 0.0 20.2 1.0 C7' A:6FU2656 1.4 17.2 1.0 F2' A:6FU2656 2.2 20.1 1.0 F3' A:6FU2656 2.2 20.4 1.0 OP1 A:A2654 2.2 6.7 0.2 S2' A:6FU2656 2.7 16.1 1.0 O2 A:6FU2656 2.9 11.7 1.0 C1' A:6FU2656 3.2 11.4 1.0 C8 A:A2654 3.3 7.1 1.0 C2' A:6FU2656 3.3 11.7 1.0 N7 A:A2654 3.5 7.3 1.0 O A:HOH2842 3.6 13.9 0.8 P A:A2654 3.7 6.6 0.2 C2 A:6FU2656 3.8 10.7 1.0 O5' A:A2654 3.9 10.3 0.8 N1 A:6FU2656 4.0 9.8 1.0 O A:HOH2707 4.1 11.2 1.0 O4' A:6FU2656 4.3 10.7 1.0 N6 A:A2665 4.4 9.9 1.0 N9 A:A2654 4.4 7.1 1.0 O4' A:A2654 4.4 7.9 1.0 O3' A:U2653 4.4 9.7 0.8 C2' A:U2653 4.4 7.7 1.0 O3' A:U2653 4.5 6.8 0.2 C5' A:A2654 4.5 10.7 0.8 OP2 A:A2654 4.5 8.0 0.2 O5' A:A2654 4.6 6.4 0.2 P A:A2654 4.6 9.5 0.8 OP1 A:A2654 4.7 10.5 0.8 C5 A:A2654 4.7 7.0 1.0 C5' A:A2654 4.7 7.9 0.2 O2' A:U2653 4.7 8.5 1.0 C3' A:6FU2656 4.7 10.4 1.0 O A:HOH2725 4.7 22.6 1.0 C3' A:U2653 4.8 7.7 1.0 N3 A:6FU2656 4.9 10.5 1.0 C4' A:6FU2656 5.0 10.6 1.0

Fluorine binding site 2 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxyuridine-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'-Deoxyuridine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2656 b:20.1 occ:1.00 F2' A:6FU2656 0.0 20.1 1.0 C7' A:6FU2656 1.4 17.2 1.0 F3' A:6FU2656 2.2 20.4 1.0 F1' A:6FU2656 2.2 20.2 1.0 S2' A:6FU2656 2.7 16.1 1.0 O2 A:6FU2656 2.8 11.7 1.0 O A:HOH2725 3.0 22.6 1.0 O4' A:A2657 3.0 10.1 1.0 C2' A:6FU2656 3.1 11.7 1.0 N6 A:A2665 3.2 9.9 1.0 C1' A:6FU2656 3.8 11.4 1.0 C4' A:A2657 4.0 10.8 1.0 C2 A:6FU2656 4.0 10.7 1.0 C1' A:A2657 4.0 9.6 1.0 C5' A:A2657 4.1 12.1 1.0 OP1 A:A2654 4.3 6.7 0.2 N1 A:6FU2656 4.4 9.8 1.0 C3' A:6FU2656 4.5 10.4 1.0 C6 A:A2665 4.5 9.6 1.0 N9 A:A2657 4.6 8.5 1.0 C8 A:A2657 4.6 8.5 1.0 O A:HOH2842 4.6 13.9 0.8 O5' A:A2657 4.7 11.5 1.0 O A:HOH2707 4.8 11.2 1.0 O3' A:6FU2656 4.8 12.7 1.0 N7 A:A2654 5.0 7.3 1.0

Fluorine binding site 3 out of 3 in the 2'-Trifluoromethylthio-2'-Deoxyuridine-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'-Deoxyuridine-Modified Srl within 5.0Å range: probe atom residue distance (Å) B Occ A:F2656 b:20.4 occ:1.00 F3' A:6FU2656 0.0 20.4 1.0 C7' A:6FU2656 1.3 17.2 1.0 F2' A:6FU2656 2.2 20.1 1.0 F1' A:6FU2656 2.2 20.2 1.0 S2' A:6FU2656 2.6 16.1 1.0 O A:HOH2842 3.0 13.9 0.8 OP1 A:A2654 3.4 6.7 0.2 C2' A:6FU2656 4.1 11.7 1.0 O A:HOH2725 4.1 22.6 1.0 P A:A2654 4.5 6.6 0.2 O2 A:6FU2656 4.5 11.7 1.0 C1' A:6FU2656 4.6 11.4 1.0 OP2 A:A2654 4.7 8.0 0.2 OP1 A:A2654 4.8 10.5 0.8 O4' A:A2657 4.9 10.1 1.0

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