Bromine in PDB 6cy0: Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.

The structure of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U., PDB code: 6cy0 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)	42.60 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.012, 47.631, 100.744, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.2

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

Fluorine

(F)

8 atoms

The binding sites of Bromine atom in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. (pdb code 6cy0). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U., PDB code: 6cy0:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:13.2 occ:0.41 BR A:CBV1 0.0 13.2 0.4 C5 A:CBV1 1.9 12.4 1.0 HN42 A:CBV1 2.5 15.6 1.0 C4 A:CBV1 2.9 9.1 1.0 C6 A:CBV1 2.9 10.1 1.0 N4 A:CBV1 3.0 13.0 1.0 H5'' C:G8 3.1 25.7 1.0 O C:HOH104 3.2 32.0 1.0 H3' C:C7 3.4 20.3 1.0 H2' C:C7 3.6 20.9 1.0 C8 C:G8 3.6 7.1 1.0 H8 C:G8 3.6 8.6 1.0 C6 C:C7 3.7 16.4 1.0 C5 C:C7 3.7 13.5 1.0 O4' C:G8 3.8 20.7 1.0 O5' C:G8 3.8 15.4 1.0 C5' C:G8 3.9 21.4 1.0 N7 C:G8 3.9 11.0 1.0 H6 C:C7 3.9 19.7 1.0 H5 C:C7 4.0 16.2 1.0 N9 C:G8 4.0 11.8 1.0 HN41 A:CBV1 4.0 15.6 1.0 N1 C:C7 4.0 14.8 1.0 C4 C:C7 4.1 11.1 1.0 N3 A:CBV1 4.1 14.8 1.0 N1 A:CBV1 4.2 11.7 1.0 C3' C:C7 4.2 16.8 1.0 C2' C:C7 4.3 17.4 1.0 C2 C:C7 4.3 9.2 1.0 N3 C:C7 4.3 9.4 1.0 OP2 C:G8 4.4 15.3 1.0 C5 C:G8 4.4 10.8 1.0 C4' C:G8 4.4 18.1 1.0 C4 C:G8 4.5 10.1 1.0 C1' C:G8 4.5 17.8 1.0 H5' C:G8 4.7 25.7 1.0 C2 A:CBV1 4.7 11.5 1.0 P C:G8 4.7 18.2 1.0 N4 C:C7 4.7 8.3 1.0 C1' C:C7 4.7 18.4 1.0 O5' C:C7 4.8 31.7 1.0 H41 C:C7 4.9 10.0 1.0 O3' C:C7 4.9 20.2 1.0

Bromine binding site 2 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1 b:13.1 occ:0.50 BR B:CBV1 0.0 13.1 0.5 C5 B:CBV1 1.9 8.1 1.0 HN42 B:CBV1 2.5 7.1 1.0 C4 B:CBV1 2.9 10.3 1.0 C6 B:CBV1 2.9 8.2 1.0 N4 B:CBV1 3.0 5.9 1.0 O B:HOH120 3.6 12.6 1.0 HN41 B:CBV1 4.0 7.1 1.0 N3 B:CBV1 4.2 7.7 1.0 N1 B:CBV1 4.2 16.1 1.0 C2 B:CBV1 4.7 10.3 1.0

Bromine binding site 3 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ C:Br1 b:7.2 occ:0.42 BR C:CBV1 0.0 7.2 0.4 C5 C:CBV1 1.9 8.9 1.0 HN42 C:CBV1 2.5 7.9 1.0 C4 C:CBV1 2.8 9.8 1.0 C6 C:CBV1 2.8 8.4 1.0 N4 C:CBV1 3.0 6.5 1.0 O C:HOH115 3.7 17.9 1.0 HN41 C:CBV1 4.0 7.9 1.0 N3 C:CBV1 4.1 6.8 1.0 N1 C:CBV1 4.2 13.4 1.0 C2 C:CBV1 4.6 11.7 1.0

Bromine binding site 4 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ D:Br1 b:10.0 occ:0.42 BR D:CBV1 0.0 10.0 0.4 C5 D:CBV1 1.9 7.6 1.0 HN42 D:CBV1 2.5 11.4 1.0 C4 D:CBV1 2.8 9.7 1.0 C6 D:CBV1 2.9 7.2 1.0 N4 D:CBV1 3.0 9.4 1.0 H5'' B:G8 3.1 23.9 1.0 O B:HOH114 3.2 27.4 1.0 H3' B:C7 3.3 17.0 1.0 H8 B:G8 3.5 14.0 1.0 C8 B:G8 3.6 11.6 1.0 O4' B:G8 3.7 10.7 1.0 H2' B:C7 3.7 16.4 1.0 O5' B:G8 3.7 18.3 1.0 C6 B:C7 3.8 9.2 1.0 C5' B:G8 3.8 19.8 1.0 C5 B:C7 3.8 7.5 1.0 N7 B:G8 3.9 9.9 1.0 H6 B:C7 3.9 11.0 1.0 N9 B:G8 3.9 12.7 1.0 H5 B:C7 4.0 9.1 1.0 HN41 D:CBV1 4.0 11.4 1.0 C3' B:C7 4.1 14.1 1.0 N3 D:CBV1 4.1 8.6 1.0 N1 B:C7 4.2 8.9 1.0 N1 D:CBV1 4.2 10.7 1.0 OP2 B:G8 4.2 16.0 1.0 C4 B:C7 4.3 6.1 1.0 C2' B:C7 4.3 13.6 1.0 C4' B:G8 4.3 14.7 1.0 C5 B:G8 4.4 6.8 1.0 C4 B:G8 4.4 7.7 1.0 C1' B:G8 4.4 15.6 1.0 P B:G8 4.5 12.6 1.0 C2 B:C7 4.6 14.1 1.0 N3 B:C7 4.6 7.6 1.0 H5' B:G8 4.6 23.9 1.0 C2 D:CBV1 4.7 12.2 1.0 H3' B:G8 4.7 20.9 1.0 O5' B:C7 4.7 18.5 1.0 O3' B:C7 4.7 18.4 1.0 C1' B:C7 4.8 16.8 1.0 N4 B:C7 4.9 5.4 1.0

Bromine binding site 5 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ E:Br1 b:10.1 occ:0.44 BR E:CBV1 0.0 10.1 0.4 C5 E:CBV1 1.9 13.5 1.0 HN42 E:CBV1 2.5 13.5 1.0 C4 E:CBV1 2.9 9.3 1.0 C6 E:CBV1 2.9 5.9 1.0 N4 E:CBV1 3.0 11.2 1.0 O E:HOH112 3.4 26.4 1.0 HN41 E:CBV1 4.0 13.5 1.0 N3 E:CBV1 4.2 8.0 1.0 N1 E:CBV1 4.2 12.7 1.0 C2 E:CBV1 4.7 12.5 1.0

Bromine binding site 6 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ F:Br1 b:14.9 occ:0.49 BR F:CBV1 0.0 14.9 0.5 C5 F:CBV1 1.9 8.7 1.0 HN42 F:CBV1 2.5 14.1 1.0 C6 F:CBV1 2.8 10.2 1.0 C4 F:CBV1 2.9 16.3 1.0 N4 F:CBV1 3.0 11.7 1.0 O F:HOH114 3.5 21.4 1.0 HN41 F:CBV1 4.0 14.1 1.0 N3 F:CBV1 4.2 10.9 1.0 N1 F:CBV1 4.2 15.2 1.0 C2 F:CBV1 4.7 12.4 1.0

Bromine binding site 7 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ G:Br1 b:10.9 occ:0.42 BR G:CBV1 0.0 10.9 0.4 C5 G:CBV1 1.9 9.8 1.0 HN42 G:CBV1 2.5 9.2 1.0 C4 G:CBV1 2.9 7.5 1.0 C6 G:CBV1 2.9 14.7 1.0 N4 G:CBV1 3.0 7.6 1.0 HN41 G:CBV1 4.0 9.2 1.0 N3 G:CBV1 4.1 10.4 1.0 N1 G:CBV1 4.2 13.4 1.0 C2 G:CBV1 4.7 9.4 1.0

Bromine binding site 8 out of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ H:Br1 b:15.4 occ:0.43 BR H:CBV1 0.0 15.4 0.4 C5 H:CBV1 1.9 11.3 1.0 HN42 H:CBV1 2.5 15.0 1.0 C4 H:CBV1 2.9 12.0 1.0 C6 H:CBV1 2.9 15.9 1.0 H6 H:CBV1 3.0 19.1 1.0 N4 H:CBV1 3.0 12.4 1.0 O H:HOH112 3.3 20.3 1.0 HN41 H:CBV1 4.0 15.0 1.0 N3 H:CBV1 4.1 11.3 1.0 N1 H:CBV1 4.2 13.7 1.0 C2 H:CBV1 4.7 8.1 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