Fluorine in PDB 6zyb: Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification

The structure of Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification, PDB code: 6zyb was solved by E.Ennifar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 0.90
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	29.500, 29.500, 77.130, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 14.9

The binding sites of Fluorine atom in the Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification (pdb code 6zyb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification, PDB code: 6zyb:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:25.5 occ:1.00 F1' A:QSK2667 0.0 25.5 1.0 C7' A:QSK2667 1.4 24.9 1.0 F3' A:QSK2667 2.2 25.2 1.0 O2' A:QSK2667 2.2 21.7 1.0 F2' A:QSK2667 2.2 27.1 1.0 H5' A:G2668 2.7 20.4 1.0 C2' A:QSK2667 2.9 19.1 1.0 O4' A:G2668 3.2 14.4 1.0 H4' A:G2668 3.4 18.1 1.0 O2 A:QSK2667 3.5 18.5 1.0 C5' A:G2668 3.5 17.0 1.0 C4' A:G2668 3.6 15.2 1.0 H1'1 A:QSK2667 3.8 20.8 1.0 C1' A:QSK2667 3.9 17.4 1.0 O3' A:QSK2667 4.1 19.5 1.0 C3' A:QSK2667 4.1 18.4 1.0 H5'' A:G2668 4.2 20.4 1.0 O5' A:G2668 4.3 18.4 1.0 C1' A:G2668 4.4 12.9 1.0 H1' A:G2668 4.4 15.4 1.0 C2 A:QSK2667 4.4 16.3 1.0 O A:HOH2710 4.5 20.0 0.6 O A:HOH2717 4.5 30.1 1.0 N1 A:QSK2667 4.6 15.1 1.0 H3'1 A:QSK2667 4.7 22.1 1.0 H8 A:G2668 4.8 13.9 1.0 H4'1 A:QSK2667 4.8 21.6 1.0 P A:G2668 4.8 20.0 1.0 C4' A:QSK2667 4.9 18.1 1.0

Fluorine binding site 2 out of 3 in the Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:27.1 occ:1.00 F2' A:QSK2667 0.0 27.1 1.0 C7' A:QSK2667 1.4 24.9 1.0 F3' A:QSK2667 2.2 25.2 1.0 F1' A:QSK2667 2.2 25.5 1.0 O2' A:QSK2667 2.3 21.7 1.0 H1'1 A:QSK2667 2.4 20.8 1.0 O A:HOH2710 2.7 20.0 0.6 O2 A:QSK2667 2.8 18.5 1.0 C2' A:QSK2667 2.9 19.1 1.0 C1' A:QSK2667 3.1 17.4 1.0 C2 A:QSK2667 3.8 16.3 1.0 N1 A:QSK2667 4.0 15.1 1.0 O4' A:QSK2667 4.1 17.9 1.0 C3' A:QSK2667 4.4 18.4 1.0 H4'1 A:QSK2667 4.4 21.6 1.0 C4' A:QSK2667 4.5 18.1 1.0 O A:HOH2717 4.6 30.1 1.0 H5' A:G2668 4.7 20.4 1.0 O4' A:G2668 4.7 14.4 1.0 O3' A:QSK2667 4.8 19.5 1.0

Fluorine binding site 3 out of 3 in the Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sarcin-Ricin Loop Rna From Ecoli with A C2667-2'-OCF3 Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:F2667 b:25.2 occ:1.00 F3' A:QSK2667 0.0 25.2 1.0 C7' A:QSK2667 1.4 24.9 1.0 F1' A:QSK2667 2.2 25.5 1.0 F2' A:QSK2667 2.2 27.1 1.0 O2' A:QSK2667 2.2 21.7 1.0 C2' A:QSK2667 3.5 19.1 1.0 H1'1 A:QSK2667 4.1 20.8 1.0 H5' A:G2668 4.1 20.4 1.0 H4'1 A:QSK2667 4.4 21.6 1.0 C1' A:QSK2667 4.4 17.4 1.0 O3' A:QSK2667 4.5 19.5 1.0 C3' A:QSK2667 4.6 18.4 1.0 O2 A:QSK2667 4.7 18.5 1.0 O A:HOH2710 4.8 20.0 0.6 C4' A:QSK2667 4.9 18.1 1.0

M.Himmelstoss, K.Erharter, E.Renard, E.Ennifar, C.Kreutz, R.Micura. 2'-O-Trifluoromethylated Rna - A Powerful Modification For Rna Chemistry and uc(Nmr) Spectroscopy Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04520A