Fluorine in PDB 6cxz: Rna Octamer Containing 2'-F, 4'-Calpha-Me U.

The structure of Rna Octamer Containing 2'-F, 4'-Calpha-Me U., PDB code: 6cxz was solved by J.M.Harp, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.44 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	30.460, 30.460, 81.889, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.5

The structure of Rna Octamer Containing 2'-F, 4'-Calpha-Me U. also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Arsenic	(As)	1 atom

The binding sites of Fluorine atom in the Rna Octamer Containing 2'-F, 4'-Calpha-Me U. (pdb code 6cxz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Rna Octamer Containing 2'-F, 4'-Calpha-Me U., PDB code: 6cxz:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Rna Octamer Containing 2'-F, 4'-Calpha-Me U.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rna Octamer Containing 2'-F, 4'-Calpha-Me U. within 5.0Å range: probe atom residue distance (Å) B Occ A:F5 b:15.1 occ:1.00 F2' A:U4M5 0.0 15.1 1.0 C2' A:U4M5 1.4 14.3 1.0 H2' A:U4M5 2.0 17.1 1.0 HM2 A:U4M5 2.2 18.7 1.0 H1' A:U4M5 2.3 17.5 1.0 C1' A:U4M5 2.3 14.7 1.0 H6M A:U4M5 2.4 17.4 1.0 C3' A:U4M5 2.4 14.6 1.0 H5' A:U6 2.6 16.5 1.0 CM A:U4M5 2.8 15.7 1.0 O3' A:U4M5 2.8 14.5 1.0 C4' A:U4M5 2.9 15.1 1.0 HM1 A:U4M5 3.0 18.7 1.0 O4' A:U4M5 3.1 14.8 1.0 O4' A:U6 3.3 14.2 1.0 H3' A:U4M5 3.3 17.5 1.0 C5' A:U6 3.3 13.8 1.0 N1 A:U4M5 3.6 14.4 1.0 O5' A:U6 3.6 13.6 1.0 O2 A:U4M5 3.8 17.1 1.0 HM3 A:U4M5 3.8 18.7 1.0 H6 A:U6 3.8 16.7 1.0 C4' A:U6 3.8 14.4 1.0 P A:U6 3.9 14.4 1.0 H4' A:U6 4.1 17.3 1.0 H5'' A:U6 4.1 16.5 1.0 C2 A:U4M5 4.1 15.1 1.0 C5' A:U4M5 4.3 15.5 1.0 C6 A:U6 4.5 14.0 1.0 C1' A:U6 4.6 14.6 1.0 H6L A:U4M5 4.6 18.5 1.0 C6 A:U4M5 4.7 14.1 1.0 H6 A:U4M5 4.8 16.9 1.0 OP1 A:U6 4.8 15.6 1.0 OP2 A:U6 4.8 15.4 1.0 H1' A:U6 4.8 17.4 1.0 N1 A:U6 4.9 13.7 1.0 H5' A:U4M5 5.0 18.5 1.0

Fluorine binding site 2 out of 2 in the Rna Octamer Containing 2'-F, 4'-Calpha-Me U.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rna Octamer Containing 2'-F, 4'-Calpha-Me U. within 5.0Å range: probe atom residue distance (Å) B Occ B:F5 b:19.5 occ:1.00 F2' B:U4M5 0.0 19.5 1.0 C2' B:U4M5 1.4 18.9 1.0 H2' B:U4M5 2.0 22.7 1.0 HM3 B:U4M5 2.2 25.1 1.0 H6M B:U4M5 2.3 25.9 1.0 C1' B:U4M5 2.4 17.7 1.0 H1' B:U4M5 2.4 21.1 1.0 C3' B:U4M5 2.4 19.9 1.0 H5' B:U6 2.6 26.3 1.0 CM B:U4M5 2.7 21.0 1.0 O3' B:U4M5 2.8 21.6 1.0 HM2 B:U4M5 2.8 25.1 1.0 C4' B:U4M5 2.9 19.8 1.0 O4' B:U4M5 3.1 18.4 1.0 H3' B:U4M5 3.4 23.9 1.0 C5' B:U6 3.4 22.0 1.0 O4' B:U6 3.5 20.0 1.0 N1 B:U4M5 3.6 16.3 1.0 HM1 B:U4M5 3.8 25.1 1.0 O2 B:U4M5 3.8 16.8 1.0 O5' B:U6 3.8 22.5 1.0 C4' B:U6 3.9 20.8 1.0 P B:U6 4.0 24.1 1.0 H4' B:U6 4.0 24.9 1.0 C2 B:U4M5 4.1 16.3 1.0 H5'' B:U6 4.1 26.3 1.0 C5' B:U4M5 4.3 19.4 1.0 H6 B:U6 4.5 20.8 1.0 H5' B:U4M5 4.7 23.2 1.0 C6 B:U4M5 4.7 15.3 1.0 H6 B:U4M5 4.8 18.4 1.0 OP1 B:U6 4.8 25.6 1.0 C1' B:U6 4.8 19.4 1.0 OP2 B:U6 4.9 26.2 1.0 H1' B:U6 4.9 23.2 1.0 H6L B:U4M5 4.9 23.2 1.0

J.M.Harp, D.C.Guenther, A.Bisbe, L.Perkins, S.Matsuda, G.R.Bommineni, I.Zlatev, D.J.Foster, N.Taneja, K.Charisse, M.A.Maier, K.G.Rajeev, M.Manoharan, M.Egli. Structural Basis For the Synergy of 4'- and 2'-Modifications on Sirna Nuclease Resistance, Thermal Stability and Rnai Activity. Nucleic Acids Res. V. 46 8090 2018.
ISSN: ESSN 1362-4962
PubMed: 30107495
DOI: 10.1093/NAR/GKY703