Bromine in PDB 5v2h: Rna Octamer Containing Glycol Nucleic Acid, Sgnt

The structure of Rna Octamer Containing Glycol Nucleic Acid, Sgnt, PDB code: 5v2h 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)	33.78 / 1.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.029, 31.901, 33.782, 90.00, 90.46, 90.00
R / Rfree (%)	13.6 / 15.7

The structure of Rna Octamer Containing Glycol Nucleic Acid, Sgnt also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Bromine atom in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt (pdb code 5v2h). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt, PDB code: 5v2h:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt


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 Glycol Nucleic Acid, Sgnt within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:8.5 occ:0.58 BR A:CBV1 0.0 8.5 0.6 C5 A:CBV1 1.9 8.0 1.0 HN41 A:CBV1 2.6 9.4 1.0 C4 A:CBV1 2.9 7.3 1.0 C6 A:CBV1 2.9 8.1 1.0 H2' D:G8 3.0 8.9 1.0 H6 A:CBV1 3.0 9.7 1.0 N4 A:CBV1 3.1 7.8 1.0 O D:HOH239 3.4 26.7 1.0 H3' D:G8 3.4 8.9 1.0 C4 D:G8 3.8 6.1 1.0 N9 D:G8 3.8 6.5 1.0 C2' D:G8 3.8 7.4 1.0 C8 D:G8 3.8 6.6 1.0 O A:HOH117 3.8 23.5 1.0 C5 D:G8 3.9 6.0 1.0 N7 D:G8 3.9 6.5 1.0 C3' D:G8 4.0 7.4 1.0 N3 A:CBV1 4.1 7.3 1.0 N1 A:CBV1 4.2 7.6 1.0 O B:HOH247 4.2 13.0 1.0 H8 D:G8 4.2 7.9 1.0 N3 D:G8 4.3 6.0 1.0 C1' D:G8 4.4 6.8 1.0 O A:HOH109 4.4 24.6 1.0 C6 D:G8 4.5 6.0 1.0 O5' A:CBV1 4.5 9.7 1.0 O3' D:G8 4.6 8.3 1.0 C2 A:CBV1 4.7 7.4 1.0 HO3' D:G8 4.7 9.9 1.0 O D:HOH205 4.8 24.1 1.0 C2 D:G8 4.8 6.2 1.0 O B:HOH218 4.8 8.1 1.0 N1 D:G8 4.9 6.0 1.0 O2' D:G8 4.9 7.9 1.0 H3' A:CBV1 4.9 9.3 1.0

Bromine binding site 2 out of 4 in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt


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 Glycol Nucleic Acid, Sgnt within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1 b:10.6 occ:0.47 BR B:CBV1 0.0 10.6 0.5 C5 B:CBV1 1.9 10.1 1.0 HN41 B:CBV1 2.6 11.6 1.0 C6 B:CBV1 2.8 10.2 1.0 C4 B:CBV1 2.9 9.3 1.0 H6 B:CBV1 2.9 12.3 1.0 N4 B:CBV1 3.1 9.7 1.0 O B:HOH249 3.6 28.8 1.0 O B:HOH211 3.8 26.2 1.0 N1 B:CBV1 4.1 10.2 1.0 N3 B:CBV1 4.1 9.6 1.0 O B:HOH215 4.3 24.5 1.0 O5' B:CBV1 4.3 16.9 1.0 C2 B:CBV1 4.6 9.6 1.0 H3' B:CBV1 4.9 13.3 1.0

Bromine binding site 3 out of 4 in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt


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 Glycol Nucleic Acid, Sgnt within 5.0Å range: probe atom residue distance (Å) B Occ C:Br1 b:8.3 occ:0.58 BR C:CBV1 0.0 8.3 0.6 C5 C:CBV1 1.8 7.5 1.0 HN41 C:CBV1 2.6 8.8 1.0 C6 C:CBV1 2.8 8.0 1.0 C4 C:CBV1 2.9 7.3 1.0 H6 C:CBV1 2.9 9.6 1.0 H2' B:G8 3.1 10.6 1.0 N4 C:CBV1 3.1 7.3 1.0 H3' B:G8 3.1 10.3 1.0 O B:HOH209 3.4 9.4 1.0 O B:HOH260 3.5 21.0 1.0 O B:HOH222 3.5 20.0 1.0 O B:HOH240 3.6 10.9 1.0 O C:HOH114 3.6 10.7 1.0 N9 B:G8 3.7 6.8 1.0 C8 B:G8 3.7 6.7 1.0 C2' B:G8 3.8 8.8 1.0 C3' B:G8 3.8 8.6 1.0 O C:HOH120 3.8 17.6 1.0 C4 B:G8 3.9 6.5 1.0 O C:HOH123 3.9 9.8 1.0 N7 B:G8 3.9 6.5 1.0 C5 B:G8 3.9 6.6 1.0 H8 B:G8 4.0 8.0 1.0 N1 C:CBV1 4.1 7.6 1.0 N3 C:CBV1 4.1 7.5 1.0 O5' C:CBV1 4.3 11.6 1.0 C1' B:G8 4.3 7.3 1.0 O3' B:G8 4.3 10.7 1.0 N3 B:G8 4.5 6.8 1.0 HO3' B:G8 4.5 12.9 1.0 C2 C:CBV1 4.6 7.3 1.0 C6 B:G8 4.7 6.4 1.0 HN31 B:NCO101 4.8 8.8 1.0 H3' C:CBV1 4.8 11.0 1.0 N7 C:G2 4.8 7.3 1.0 O5' B:G8 5.0 7.5 1.0

Bromine binding site 4 out of 4 in the Rna Octamer Containing Glycol Nucleic Acid, Sgnt


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 Glycol Nucleic Acid, Sgnt within 5.0Å range: probe atom residue distance (Å) B Occ D:Br1 b:7.7 occ:0.40 BR D:CBV1 0.0 7.7 0.4 C5 D:CBV1 1.9 8.7 1.0 HN41 D:CBV1 2.6 9.8 1.0 C4 D:CBV1 2.9 8.4 1.0 C6 D:CBV1 2.9 8.7 1.0 H6 D:CBV1 3.0 10.5 1.0 N4 D:CBV1 3.0 8.2 1.0 O D:HOH240 3.5 16.4 1.0 O D:HOH232 3.7 33.7 1.0 O D:HOH215 3.7 13.9 1.0 O D:HOH230 4.1 12.6 1.0 N3 D:CBV1 4.1 8.3 1.0 N1 D:CBV1 4.2 8.3 1.0 O5' D:CBV1 4.4 10.8 1.0 C2 D:CBV1 4.7 7.9 1.0 H3' D:CBV1 4.9 10.5 1.0

M.K.Schlegel, D.J.Foster, A.V.Kel'in, I.Zlatev, A.Bisbe, M.Jayaraman, J.G.Lackey, K.G.Rajeev, K.Charisse, J.Harp, P.S.Pallan, M.A.Maier, M.Egli, M.Manoharan. Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on Sirna. J. Am. Chem. Soc. V. 139 8537 2017.
ISSN: ESSN 1520-5126
PubMed: 28570818
DOI: 10.1021/JACS.7B02694