Fluorine in PDB 4nxh: 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop

The structure of 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop, PDB code: 4nxh 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)	29.56 / 1.16
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	29.560, 29.560, 76.730, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 14.8

The binding sites of Fluorine atom in the 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop (pdb code 4nxh). 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'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop, PDB code: 4nxh:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:F2650 b:19.5 occ:1.00 F1' A:6FU2650 0.0 19.5 1.0 C7' A:6FU2650 1.3 19.0 1.0 F3' A:6FU2650 2.1 19.2 1.0 F2' A:6FU2650 2.2 22.0 1.0 S2' A:6FU2650 2.6 17.0 1.0 H8 A:6FU2650 2.6 16.0 1.0 O A:HOH2820 2.7 19.2 1.0 O4' A:C2651 2.7 11.3 1.0 H1' A:C2651 2.9 12.7 1.0 C2' A:6FU2650 3.1 13.3 1.0 O2 A:6FU2650 3.3 12.5 1.0 C1' A:C2651 3.3 10.6 1.0 H4' A:C2651 3.4 13.8 1.0 C4' A:C2651 3.6 11.5 1.0 H9 A:6FU2650 3.6 15.4 1.0 HO2' A:C2651 3.9 14.2 1.0 H5' A:C2651 3.9 15.3 1.0 C1' A:6FU2650 3.9 12.9 1.0 N1 A:C2651 4.3 9.9 1.0 C5' A:C2651 4.3 12.7 1.0 C2 A:6FU2650 4.3 11.7 1.0 C3' A:6FU2650 4.5 12.4 1.0 C2' A:C2651 4.5 10.4 1.0 O2' A:C2651 4.5 11.8 1.0 H6 A:C2651 4.6 12.8 1.0 N1 A:6FU2650 4.6 11.8 1.0 O3' A:6FU2650 4.7 13.6 1.0 H22 A:G2671 4.8 33.9 1.0 C6 A:C2651 4.8 10.7 1.0 C3' A:C2651 4.8 10.5 1.0 H2 A:A2670 4.8 14.2 1.0 O5' A:C2651 4.8 13.1 1.0 H6 A:6FU2650 4.9 14.8 1.0 O A:HOH2813 5.0 16.4 1.0

Fluorine binding site 2 out of 3 in the 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:F2650 b:22.0 occ:1.00 F2' A:6FU2650 0.0 22.0 1.0 C7' A:6FU2650 1.3 19.0 1.0 F3' A:6FU2650 2.2 19.2 1.0 F1' A:6FU2650 2.2 19.5 1.0 S2' A:6FU2650 2.5 17.0 1.0 C2' A:6FU2650 4.0 13.3 1.0 H8 A:6FU2650 4.0 16.0 1.0 H9 A:6FU2650 4.1 15.4 1.0 O A:HOH2820 4.3 19.2 1.0 H5' A:C2651 4.5 15.3 1.0 O4' A:C2651 4.5 11.3 1.0 C1' A:6FU2650 4.6 12.9 1.0 H4' A:C2651 4.7 13.8 1.0 O2 A:6FU2650 4.9 12.5 1.0 H22 A:G2671 5.0 33.9 1.0

Fluorine binding site 3 out of 3 in the 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 2'-Trifluoromethylthiouridine-Modified E. Coli 23S Rrna Sarcin Ricin Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:F2650 b:19.2 occ:1.00 F3' A:6FU2650 0.0 19.2 1.0 C7' A:6FU2650 1.3 19.0 1.0 F1' A:6FU2650 2.1 19.5 1.0 F2' A:6FU2650 2.2 22.0 1.0 H9 A:6FU2650 2.4 15.4 1.0 S2' A:6FU2650 2.5 17.0 1.0 H22 A:G2671 2.9 33.9 1.0 O2 A:6FU2650 3.1 12.5 1.0 C2' A:6FU2650 3.1 13.3 1.0 H8 A:6FU2650 3.2 16.0 1.0 C1' A:6FU2650 3.2 12.9 1.0 O A:HOH2820 3.2 19.2 1.0 N2 A:G2671 3.6 28.2 1.0 C2 A:6FU2650 3.9 11.7 1.0 H21 A:G2671 4.0 33.9 1.0 N1 A:6FU2650 4.0 11.8 1.0 O4' A:6FU2650 4.2 13.5 1.0 O A:HOH2855 4.3 26.0 1.0 N3 A:G2671 4.3 26.5 1.0 C2 A:G2671 4.3 27.1 1.0 O4' A:C2651 4.5 11.3 1.0 C3' A:6FU2650 4.6 12.4 1.0 H1' A:C2651 4.7 12.7 1.0 H5 A:6FU2650 4.7 16.1 0.5 C4' A:6FU2650 4.8 13.4 1.0 H5 A:6FU2650 4.8 16.1 0.5

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