Fluorine in PDB 5vr4: Rna Octamer Containing 2'-F-4'-Ome U.

The structure of Rna Octamer Containing 2'-F-4'-Ome U., PDB code: 5vr4 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)	29.48 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	44.387, 44.387, 85.921, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.3

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

Cobalt

(Co)

1 atom

The binding sites of Fluorine atom in the Rna Octamer Containing 2'-F-4'-Ome U. (pdb code 5vr4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Rna Octamer Containing 2'-F-4'-Ome U., PDB code: 5vr4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Rna Octamer Containing 2'-F-4'-Ome 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'-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ A:F105 b:19.8 occ:1.00 F2' A:UMO105 0.0 19.8 1.0 C2' A:UMO105 1.4 19.2 1.0 H2' A:UMO105 2.0 23.0 1.0 C1' A:UMO105 2.3 18.4 1.0 C3' A:UMO105 2.4 18.8 1.0 H1' A:UMO105 2.4 22.1 1.0 OM1 A:UMO105 2.7 22.4 1.0 O3' A:UMO105 2.8 19.1 1.0 H5' A:U106 2.9 23.6 1.0 C4' A:UMO105 3.0 20.0 1.0 O4' A:UMO105 3.0 18.9 1.0 O D:HOH330 3.1 32.2 1.0 O2' D:A211 3.2 19.1 1.0 HO2' D:A211 3.3 22.9 1.0 O4' A:U106 3.3 19.0 1.0 H3' A:UMO105 3.3 22.6 1.0 O A:HOH204 3.4 30.5 1.0 N1 A:UMO105 3.5 17.1 1.0 C5' A:U106 3.6 19.7 1.0 CM1 A:UMO105 3.7 23.8 1.0 O2 A:UMO105 3.7 21.4 1.0 O5' A:U106 3.7 20.2 1.0 O A:HOH230 3.7 33.0 1.0 HM1 A:UMO105 3.8 28.6 1.0 H6 A:U106 3.8 23.4 1.0 P A:U106 3.9 22.0 1.0 H6M A:UMO105 3.9 28.6 1.0 C4' A:U106 4.0 19.3 1.0 C2 A:UMO105 4.1 18.9 1.0 H4' D:A211 4.2 23.1 1.0 H4' A:U106 4.4 23.1 1.0 C6 A:U106 4.4 19.5 1.0 H5'' A:U106 4.4 23.6 1.0 C5' A:UMO105 4.4 20.6 1.0 C1' A:U106 4.5 20.1 1.0 H6L A:UMO105 4.6 28.6 1.0 C2' D:A211 4.6 17.5 1.0 C6 A:UMO105 4.6 15.9 1.0 H1' D:A211 4.6 22.0 1.0 H5'' A:UMO105 4.7 24.7 1.0 H1' A:U106 4.7 24.1 1.0 H6 A:UMO105 4.7 19.1 1.0 N1 A:U106 4.7 19.5 1.0 OP2 A:U106 4.8 24.4 1.0 H5' D:A212 4.8 25.4 1.0 OP1 A:U106 4.8 23.7 1.0 C4' D:A211 5.0 19.3 1.0

Fluorine binding site 2 out of 4 in the Rna Octamer Containing 2'-F-4'-Ome 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'-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ B:F213 b:24.6 occ:1.00 F2' B:UMO213 0.0 24.6 1.0 C2' B:UMO213 1.4 23.1 1.0 H2' B:UMO213 2.1 27.7 1.0 C1' B:UMO213 2.4 21.1 1.0 C3' B:UMO213 2.4 24.3 1.0 H1' B:UMO213 2.5 25.4 1.0 OM1 B:UMO213 2.5 26.9 1.0 H5' B:U214 2.7 25.5 1.0 O3' B:UMO213 2.8 24.3 1.0 C4' B:UMO213 2.9 25.6 1.0 O4' B:UMO213 3.0 23.2 1.0 O4' B:U214 3.2 21.1 1.0 O B:HOH309 3.2 28.5 1.0 H3' B:UMO213 3.4 29.1 1.0 C5' B:U214 3.4 21.3 1.0 O C:HOH303 3.5 33.6 1.0 CM1 B:UMO213 3.5 27.0 1.0 O5' B:U214 3.6 21.0 1.0 N1 B:UMO213 3.6 19.9 1.0 H6L B:UMO213 3.6 32.4 1.0 O B:HOH332 3.7 44.0 1.0 H6 B:U214 3.8 23.1 1.0 H6M B:UMO213 3.8 32.4 1.0 O2 B:UMO213 3.8 21.2 1.0 C4' B:U214 3.8 20.3 1.0 HO2' C:G108 3.8 28.8 1.0 P B:U214 3.9 23.7 1.0 H4' B:U214 4.1 24.4 1.0 C2 B:UMO213 4.1 19.9 1.0 H5'' B:U214 4.2 25.5 1.0 O2' C:G108 4.3 24.0 1.0 C5' B:UMO213 4.4 25.7 1.0 O B:HOH307 4.4 33.2 1.0 C6 B:U214 4.4 19.2 1.0 C1' B:U214 4.4 19.9 1.0 O C:HOH312 4.5 28.6 1.0 HM1 B:UMO213 4.5 32.4 1.0 C6 B:UMO213 4.6 19.9 1.0 H5' B:UMO213 4.7 30.8 1.0 H1' B:U214 4.7 23.9 1.0 H6 B:UMO213 4.7 23.9 1.0 OP2 B:U214 4.8 26.1 1.0 N1 B:U214 4.8 17.5 1.0 OP1 B:U214 4.8 25.3 1.0 O C:HOH320 4.9 37.0 1.0

Fluorine binding site 3 out of 4 in the Rna Octamer Containing 2'-F-4'-Ome U.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rna Octamer Containing 2'-F-4'-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ C:F105 b:21.3 occ:1.00 F2' C:UMO105 0.0 21.3 1.0 C2' C:UMO105 1.4 19.4 1.0 H2' C:UMO105 2.0 23.2 1.0 C1' C:UMO105 2.4 18.1 1.0 C3' C:UMO105 2.4 18.7 1.0 H1' C:UMO105 2.5 21.7 1.0 OM1 C:UMO105 2.7 22.3 1.0 O3' C:UMO105 2.8 19.8 1.0 H5' C:U106 2.9 22.4 1.0 O4' C:UMO105 3.0 18.7 1.0 C4' C:UMO105 3.0 19.9 1.0 O4' C:U106 3.3 19.0 1.0 H3' C:UMO105 3.4 22.4 1.0 N1 C:UMO105 3.6 18.1 1.0 C5' C:U106 3.6 18.7 1.0 CM1 C:UMO105 3.6 22.9 1.0 O5' C:U106 3.7 18.3 1.0 HM1 C:UMO105 3.7 27.5 1.0 O2 C:UMO105 3.7 20.9 1.0 H6 C:U106 3.8 20.8 1.0 H6M C:UMO105 3.9 27.5 1.0 P C:U106 3.9 20.6 1.0 C4' C:U106 4.0 18.4 1.0 C2 C:UMO105 4.1 19.5 1.0 C6 C:U106 4.3 17.4 1.0 H4' C:U106 4.4 22.1 1.0 O C:HOH331 4.4 44.0 1.0 C5' C:UMO105 4.5 21.0 1.0 C1' C:U106 4.5 17.7 1.0 H5'' C:U106 4.5 22.4 1.0 H6L C:UMO105 4.6 27.5 1.0 C6 C:UMO105 4.6 17.8 1.0 H1' C:U106 4.7 21.2 1.0 N1 C:U106 4.7 17.5 1.0 H5'' C:UMO105 4.7 25.2 1.0 H6 C:UMO105 4.7 21.3 1.0 OP2 C:U106 4.8 23.8 1.0 OP1 C:U106 4.8 22.5 1.0

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rna Octamer Containing 2'-F-4'-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ D:F213 b:23.5 occ:1.00 F2' D:UMO213 0.0 23.5 1.0 C2' D:UMO213 1.4 22.7 1.0 H2' D:UMO213 2.0 27.2 1.0 C1' D:UMO213 2.4 21.8 1.0 C3' D:UMO213 2.4 22.3 1.0 H1' D:UMO213 2.5 26.2 1.0 H5' D:U214 2.6 25.1 1.0 OM1 D:UMO213 2.7 26.0 1.0 O3' D:UMO213 2.8 22.1 1.0 C4' D:UMO213 3.0 23.8 1.0 O4' D:UMO213 3.0 23.3 1.0 O D:HOH322 3.1 31.1 1.0 O4' D:U214 3.2 21.8 1.0 H3' D:UMO213 3.4 26.7 1.0 C5' D:U214 3.4 20.9 1.0 O D:HOH331 3.4 46.7 1.0 N1 D:UMO213 3.6 21.3 1.0 CM1 D:UMO213 3.6 26.5 1.0 O5' D:U214 3.6 20.1 1.0 HM1 D:UMO213 3.7 31.8 1.0 O2 D:UMO213 3.7 22.9 1.0 C4' D:U214 3.8 21.4 1.0 H6 D:U214 3.9 25.8 1.0 H6M D:UMO213 3.9 31.8 1.0 P D:U214 3.9 22.2 1.0 H4' D:U214 4.1 25.7 1.0 C2 D:UMO213 4.1 22.3 1.0 H5'' D:U214 4.2 25.1 1.0 C5' D:UMO213 4.4 22.7 1.0 C1' D:U214 4.5 21.7 1.0 C6 D:U214 4.5 21.5 1.0 H6L D:UMO213 4.6 31.8 1.0 C6 D:UMO213 4.6 19.6 1.0 H1' D:U214 4.7 26.1 1.0 H6 D:UMO213 4.7 23.5 1.0 H5' D:UMO213 4.7 27.2 1.0 OP1 D:U214 4.9 24.6 1.0 OP2 D:U214 4.9 25.1 1.0 N1 D:U214 4.9 20.5 1.0

E.Malek-Adamian, D.C.Guenther, S.Matsuda, S.Martinez-Montero, I.Zlatev, J.Harp, M.Burai Patrascu, D.J.Foster, J.Fakhoury, L.Perkins, N.Moitessier, R.M.Manoharan, N.Taneja, A.Bisbe, K.Charisse, M.Maier, K.G.Rajeev, M.Egli, M.Manoharan, M.J.Damha. 4'-C-Methoxy-2'-Deoxy-2'-Fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient Rnai-Mediated Gene Silencing. J. Am. Chem. Soc. V. 139 14542 2017.
ISSN: ESSN 1520-5126
PubMed: 28937776
DOI: 10.1021/JACS.7B07582