Bromine in PDB 8ynp: Rna Duplex Containing Methylformamide

The structure of Rna Duplex Containing Methylformamide, PDB code: 8ynp 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)	25.15 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.604, 27.932, 28.668, 110.03, 114.81, 95.76
R / Rfree (%)	15.2 / 17.3

The binding sites of Bromine atom in the Rna Duplex Containing Methylformamide (pdb code 8ynp). 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 Methylformamide, PDB code: 8ynp:
Jump to Bromine binding site number: 1; 2;

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


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 Methylformamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br5 b:11.2 occ:0.55 BR A:5BU5 0.0 11.2 0.6 C5 A:5BU5 1.9 11.1 1.0 C6 A:5BU5 2.9 11.7 1.0 C4 A:5BU5 2.9 9.3 1.0 O4 A:5BU5 3.1 10.1 1.0 O A:HOH153 3.3 16.9 1.0 C4 A:C4 3.5 8.6 1.0 C5 A:C4 3.5 8.6 1.0 N3 A:C4 3.6 8.1 1.0 O A:HOH163 3.6 19.1 1.0 O A:HOH112 3.6 17.0 1.0 C6 A:C4 3.7 8.2 1.0 OP2 A:5BU5 3.7 15.0 1.0 C2 A:C4 3.7 8.5 1.0 N1 A:C4 3.7 8.2 1.0 O A:HOH126 3.7 18.1 1.0 O A:HOH107 3.9 17.7 1.0 O A:HOH182 3.9 25.0 1.0 O A:HOH177 4.0 19.4 1.0 N4 A:C4 4.1 9.9 1.0 C2' A:C4 4.2 10.1 1.0 N1 A:5BU5 4.2 10.7 1.0 C3' A:C4 4.3 10.4 1.0 N3 A:5BU5 4.3 10.4 1.0 O2 A:C4 4.4 9.5 1.0 O5' A:5BU5 4.4 13.6 1.0 C1' A:C4 4.6 11.1 1.0 N4 A:C6 4.6 9.2 1.0 P A:5BU5 4.6 13.3 1.0 C5 A:C6 4.8 9.0 1.0 C2 A:5BU5 4.8 13.4 1.0 O3' A:C4 5.0 12.7 1.0

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


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 Methylformamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br5 b:10.4 occ:0.49 BR B:5BU5 0.0 10.4 0.5 C5 B:5BU5 1.9 10.0 1.0 C6 B:5BU5 2.9 10.6 1.0 C4 B:5BU5 2.9 10.7 1.0 O4 B:5BU5 3.1 10.9 1.0 O B:HOH147 3.4 15.6 1.0 C5 B:C4 3.5 9.3 1.0 C4 B:C4 3.6 7.7 1.0 O B:HOH107 3.6 20.4 1.0 C6 B:C4 3.6 8.8 1.0 OP2 B:5BU5 3.7 14.1 1.0 O B:HOH160 3.7 19.2 1.0 N3 B:C4 3.7 7.3 1.0 N1 B:C4 3.8 9.4 1.0 O B:HOH139 3.8 13.7 1.0 O B:HOH185 3.8 23.2 1.0 C2 B:C4 3.8 10.4 1.0 O B:HOH106 4.1 19.0 1.0 N4 B:C4 4.2 9.6 1.0 N1 B:5BU5 4.2 9.9 1.0 C3' B:C4 4.2 11.4 1.0 C2' B:C4 4.2 11.8 1.0 N3 B:5BU5 4.3 10.7 1.0 O5' B:5BU5 4.5 10.9 1.0 O2 B:C4 4.5 12.4 1.0 C1' B:C4 4.6 11.1 1.0 P B:5BU5 4.6 12.8 1.0 C2 B:5BU5 4.8 10.3 1.0 N4 B:C6 4.8 8.6 1.0 O3' B:C4 4.9 10.6 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