Bromine in PDB 6cy4: Rna Octamer Containing 2'-Ome, 4'- Cbeta-Ome U.

The structure of Rna Octamer Containing 2'-Ome, 4'- Cbeta-Ome U., PDB code: 6cy4 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)	18.73 / 1.85
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	90.438, 90.438, 64.123, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 23.1

The binding sites of Bromine atom in the Rna Octamer Containing 2'-Ome, 4'- Cbeta-Ome U. (pdb code 6cy4). 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'-Ome, 4'- Cbeta-Ome U., PDB code: 6cy4:
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'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:57.3 occ:1.00 BR A:CBV1 0.0 57.3 1.0 C5 A:CBV1 1.9 47.4 1.0 HN42 A:CBV1 2.5 49.9 1.0 C6 A:CBV1 2.8 44.9 1.0 C4 A:CBV1 2.9 43.4 1.0 H6 A:CBV1 2.9 53.9 1.0 N4 A:CBV1 3.1 41.6 1.0 H3' D:G8 3.1 56.5 1.0 H2' D:G8 3.2 56.8 1.0 C8 D:G8 3.5 39.2 1.0 N7 D:G8 3.5 38.1 1.0 C5 D:G8 3.5 37.8 1.0 N9 D:G8 3.5 40.4 1.0 C4 D:G8 3.5 38.0 1.0 C3' D:G8 3.8 47.1 1.0 C2' D:G8 3.8 47.4 1.0 H8 D:G8 3.9 47.1 1.0 HN41 A:CBV1 4.0 49.9 1.0 O5' A:CBV1 4.1 46.7 1.0 N1 A:CBV1 4.2 42.6 1.0 N3 A:CBV1 4.2 41.7 1.0 C6 D:G8 4.2 36.2 1.0 N3 D:G8 4.2 36.3 1.0 C1' D:G8 4.3 44.6 1.0 O3' D:G8 4.5 47.4 1.0 O A:HOH102 4.6 43.0 1.0 C2 A:CBV1 4.7 39.8 1.0 N1 D:G8 4.7 35.9 1.0 C2 D:G8 4.7 35.2 1.0 H3' A:CBV1 4.8 58.0 1.0 O6 D:G8 4.8 37.2 1.0 O4' D:G8 4.9 45.7 1.0 O5' D:G8 4.9 55.2 1.0 C4' D:G8 5.0 48.1 1.0

Bromine binding site 2 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1 b:48.1 occ:0.38 BR B:CBV1 0.0 48.1 0.4 C5 B:CBV1 1.9 45.7 1.0 HN42 B:CBV1 2.5 53.4 1.0 C6 B:CBV1 2.8 44.1 1.0 C4 B:CBV1 2.9 44.9 1.0 H6 B:CBV1 2.9 52.9 1.0 N4 B:CBV1 3.0 44.5 1.0 N7 F:G8 3.4 21.8 1.0 C8 F:G8 3.5 25.9 1.0 H3' F:G8 3.6 66.3 1.0 C5 F:G8 3.6 20.4 1.0 H2' F:G8 3.6 62.0 1.0 H8 F:G8 3.8 31.1 1.0 N9 F:G8 3.8 31.2 1.0 C4 F:G8 3.9 23.6 1.0 HN41 B:CBV1 4.0 53.4 1.0 N1 B:CBV1 4.1 43.2 1.0 N3 B:CBV1 4.2 44.2 1.0 O5' B:CBV1 4.2 48.2 1.0 C6 F:G8 4.3 19.0 1.0 C2' F:G8 4.3 51.7 1.0 C3' F:G8 4.3 55.3 1.0 C2 B:CBV1 4.7 43.0 1.0 C1' F:G8 4.7 41.8 1.0 O6 F:G8 4.7 20.0 1.0 N3 F:G8 4.8 20.3 1.0 O5' F:G8 5.0 55.4 1.0

Bromine binding site 3 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ C:Br1 b:40.8 occ:0.67 BR C:CBV1 0.0 40.8 0.7 C5 C:CBV1 1.9 39.6 1.0 HN42 C:CBV1 2.6 49.0 1.0 C6 C:CBV1 2.8 38.4 1.0 C4 C:CBV1 2.9 39.2 1.0 H6 C:CBV1 2.9 46.0 1.0 N4 C:CBV1 3.1 40.8 1.0 O B:HOH105 3.2 41.8 1.0 H3' B:G8 3.3 66.4 1.0 H2' B:G8 3.3 62.4 1.0 N7 B:G8 3.5 37.7 1.0 C8 B:G8 3.5 39.7 1.0 C5 B:G8 3.6 35.7 1.0 N9 B:G8 3.7 41.5 1.0 C4 B:G8 3.7 36.7 1.0 H8 B:G8 3.9 47.7 1.0 C2' B:G8 4.0 52.0 1.0 C3' B:G8 4.0 55.3 1.0 HN41 C:CBV1 4.0 49.0 1.0 O5' C:CBV1 4.1 44.0 1.0 N1 C:CBV1 4.1 37.2 1.0 N3 C:CBV1 4.2 37.6 1.0 C6 B:G8 4.2 33.5 1.0 C1' B:G8 4.4 48.8 1.0 N3 B:G8 4.4 32.8 1.0 C2 C:CBV1 4.7 37.7 1.0 O3' B:G8 4.7 56.3 1.0 O6 B:G8 4.8 33.2 1.0 N1 B:G8 4.8 32.8 1.0 C2 B:G8 4.9 33.0 1.0 H3' C:CBV1 4.9 48.2 1.0 O5' B:G8 5.0 71.0 1.0

Bromine binding site 4 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ D:Br1 b:56.1 occ:1.00 BR D:CBV1 0.0 56.1 1.0 C5 D:CBV1 1.9 52.3 1.0 HN42 D:CBV1 2.6 55.2 1.0 C6 D:CBV1 2.8 48.2 1.0 C4 D:CBV1 2.9 45.8 1.0 H6 D:CBV1 2.9 57.8 1.0 N4 D:CBV1 3.0 46.0 1.0 O D:HOH101 4.0 30.9 1.0 HN41 D:CBV1 4.0 55.2 1.0 N1 D:CBV1 4.2 44.7 1.0 N3 D:CBV1 4.2 44.0 1.0 O5' D:CBV1 4.2 37.8 1.0 O D:HOH102 4.5 30.9 1.0 C2 D:CBV1 4.7 43.2 1.0 H3' D:CBV1 4.8 50.7 1.0

Bromine binding site 5 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ E:Br1 b:55.3 occ:1.00 BR E:CBV1 0.0 55.3 1.0 C5 E:CBV1 1.9 53.4 1.0 HN42 E:CBV1 2.6 55.4 1.0 C6 E:CBV1 2.8 47.3 1.0 C4 E:CBV1 2.9 46.6 1.0 H3' A:G8 2.9 59.7 1.0 H6 E:CBV1 2.9 56.8 1.0 N4 E:CBV1 3.0 46.2 1.0 H2' A:G8 3.1 61.3 1.0 C8 A:G8 3.5 44.1 1.0 N9 A:G8 3.5 46.1 1.0 N7 A:G8 3.6 43.3 1.0 C4 A:G8 3.6 43.6 1.0 C5 A:G8 3.6 43.0 1.0 C3' A:G8 3.6 49.7 1.0 C2' A:G8 3.7 51.1 1.0 O E:HOH106 3.8 28.1 1.0 H8 A:G8 3.8 53.0 1.0 HN41 E:CBV1 4.0 55.4 1.0 O5' E:CBV1 4.1 36.2 1.0 N1 E:CBV1 4.2 43.6 1.0 N3 E:CBV1 4.2 42.9 1.0 C1' A:G8 4.2 47.7 1.0 N3 A:G8 4.3 43.9 1.0 O3' A:G8 4.4 49.3 1.0 C6 A:G8 4.4 43.6 1.0 C2 E:CBV1 4.7 42.0 1.0 O4' A:G8 4.7 47.3 1.0 H3' E:CBV1 4.8 50.9 1.0 C4' A:G8 4.8 48.5 1.0 C2 A:G8 4.8 43.2 1.0 O5' A:G8 4.8 48.7 1.0 N1 A:G8 4.9 44.7 1.0

Bromine binding site 6 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ F:Br1 b:72.4 occ:1.00 BR F:CBV1 0.0 72.4 1.0 C5 F:CBV1 1.9 66.9 1.0 HN42 F:CBV1 2.5 65.7 1.0 C6 F:CBV1 2.9 57.9 1.0 C4 F:CBV1 2.9 58.0 1.0 H6 F:CBV1 3.0 69.5 1.0 N4 F:CBV1 3.1 54.8 1.0 HN41 F:CBV1 4.1 65.7 1.0 O5' F:CBV1 4.1 41.5 1.0 N1 F:CBV1 4.2 49.0 1.0 N3 F:CBV1 4.2 51.8 1.0 C2 F:CBV1 4.7 47.0 1.0 H3' F:CBV1 4.8 55.0 1.0 N7 F:G2 4.9 37.1 1.0

Bromine binding site 7 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ G:Br1 b:61.1 occ:1.00 BR G:CBV1 0.0 61.1 1.0 C5 G:CBV1 1.9 55.5 1.0 HN42 G:CBV1 2.6 62.0 1.0 C6 G:CBV1 2.8 52.6 1.0 C4 G:CBV1 2.9 52.8 1.0 H6 G:CBV1 2.9 63.1 1.0 N4 G:CBV1 3.1 51.6 1.0 O G:HOH103 3.6 43.0 1.0 HN41 G:CBV1 4.1 62.0 1.0 O5' G:CBV1 4.1 50.5 1.0 N1 G:CBV1 4.1 49.6 1.0 N3 G:CBV1 4.2 50.2 1.0 C2 G:CBV1 4.7 48.8 1.0 H3' G:CBV1 4.7 62.1 1.0

Bromine binding site 8 out of 8 in the Rna Octamer Containing 2'-Ome, 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'-Ome, 4'- Cbeta-Ome U. within 5.0Å range: probe atom residue distance (Å) B Occ H:Br1 b:74.2 occ:1.00 BR H:CBV1 0.0 74.2 1.0 C5 H:CBV1 1.9 64.2 1.0 HN42 H:CBV1 2.6 68.9 1.0 C6 H:CBV1 2.8 57.0 1.0 C4 H:CBV1 2.9 58.2 1.0 H6 H:CBV1 2.9 68.4 1.0 N4 H:CBV1 3.1 57.4 1.0 HN41 H:CBV1 4.0 68.9 1.0 N1 H:CBV1 4.2 51.0 1.0 N3 H:CBV1 4.2 53.0 1.0 O5' H:CBV1 4.2 43.3 1.0 O H:HOH102 4.2 48.4 1.0 C2 H:CBV1 4.7 49.6 1.0 H3' H:CBV1 5.0 55.5 1.0 O H:HOH101 5.0 42.2 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