Bromine in PDB 8yno: Rna Duplex Containing Formamide

The structure of Rna Duplex Containing Formamide, PDB code: 8yno was solved by J.Kondo, H.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.43 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.633, 43.063, 28.043, 90, 109.51, 90
R / Rfree (%)	15.1 / 17.3

The binding sites of Bromine atom in the Rna Duplex Containing Formamide (pdb code 8yno). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Rna Duplex Containing Formamide, PDB code: 8yno:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Rna Duplex Containing Formamide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Duplex Containing Formamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br5 b:10.4 occ:0.56 BR A:5BU5 0.0 10.4 0.6 C5 A:5BU5 1.9 10.6 1.0 C6 A:5BU5 2.9 8.7 1.0 C4 A:5BU5 3.0 8.6 1.0 O4 A:5BU5 3.1 8.7 1.0 O A:HOH266 3.3 15.2 1.0 C5 A:C4 3.4 8.7 1.0 C4 A:C4 3.4 8.7 1.0 O A:HOH225 3.5 17.1 1.0 O A:HOH261 3.5 18.7 1.0 C6 A:C4 3.6 8.3 1.0 N3 A:C4 3.6 8.3 1.0 OP2 A:5BU5 3.6 12.8 1.0 N1 A:C4 3.7 8.9 1.0 C2 A:C4 3.7 9.2 1.0 O A:HOH218 3.7 17.7 1.0 O A:HOH204 3.9 17.4 1.0 O A:HOH284 4.0 21.0 1.0 N4 A:C4 4.0 9.3 1.0 C2' A:C4 4.2 10.5 1.0 C3' A:C4 4.2 9.5 1.0 N1 A:5BU5 4.2 10.0 1.0 N3 A:5BU5 4.3 9.5 1.0 O5' A:5BU5 4.3 10.4 1.0 O2 A:C4 4.4 9.6 1.0 P A:5BU5 4.6 11.6 1.0 C1' A:C4 4.6 9.1 1.0 C2 A:5BU5 4.8 9.9 1.0 O A:HOH281 4.9 27.7 1.0 O3' A:C4 4.9 10.8 1.0 N4 A:C6 4.9 10.3 1.0

Bromine binding site 2 out of 2 in the Rna Duplex Containing Formamide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Duplex Containing Formamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br5 b:9.9 occ:0.61 BR B:5BU5 0.0 9.9 0.6 C5 B:5BU5 1.9 8.7 1.0 C6 B:5BU5 2.9 8.2 1.0 C4 B:5BU5 2.9 9.3 1.0 O4 B:5BU5 3.1 9.7 1.0 O B:HOH133 3.1 14.5 1.0 C5 B:C4 3.4 7.8 1.0 C4 B:C4 3.6 7.4 1.0 O B:HOH166 3.6 17.6 1.0 C6 B:C4 3.6 7.5 1.0 O B:HOH113 3.6 20.1 1.0 O B:HOH149 3.7 12.7 1.0 OP2 B:5BU5 3.7 10.6 1.0 N1 B:C4 3.8 7.6 1.0 N3 B:C4 3.8 7.4 1.0 O B:HOH111 3.9 13.0 1.0 C2 B:C4 3.9 8.3 1.0 O B:HOH182 4.0 20.9 1.0 N4 B:C4 4.1 8.4 1.0 N1 B:5BU5 4.2 8.3 1.0 N3 B:5BU5 4.2 8.5 1.0 C3' B:C4 4.3 7.2 1.0 C2' B:C4 4.4 8.0 1.0 O5' B:5BU5 4.5 8.1 1.0 P B:5BU5 4.7 9.1 1.0 C1' B:C4 4.7 8.1 1.0 O2 B:C4 4.7 8.8 1.0 C2 B:5BU5 4.8 9.0 1.0 N4 B:C6 4.8 7.9 1.0 O5' B:C4 4.9 8.1 1.0 O3' B:C4 5.0 8.4 1.0

K.Nomura, S.An, Y.Kobayashi, J.Kondo, T.Shi, H.Murase, K.Nakamoto, Y.Kimura, N.Abe, K.Ui-Tei, H.Abe. Synthesis of 2'-Formamidonucleoside Phosphoramidites For Suppressing the Seed-Based Off-Target Effects of Sirnas. Nucleic Acids Res. V. 52 10754 2024.
ISSN: ESSN 1362-4962
PubMed: 39231537
DOI: 10.1093/NAR/GKAE741