Bromine in PDB 7lo9: Rna Dodecamer Containing A Gna A Residue

The structure of Rna Dodecamer Containing A Gna A Residue, PDB code: 7lo9 was solved by J.M.Harp, Z.Wawrzak, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.76 / 1.78
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	29.37, 29.37, 133.14, 90, 90, 120
R / Rfree (%)	19.5 / 22.6

The binding sites of Bromine atom in the Rna Dodecamer Containing A Gna A Residue (pdb code 7lo9). 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 Dodecamer Containing A Gna A Residue, PDB code: 7lo9:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Rna Dodecamer Containing A Gna A Residue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Dodecamer Containing A Gna A Residue within 5.0Å range: probe atom residue distance (Å) B Occ A:Br7 b:53.1 occ:0.61 BR A:5BU7 0.0 53.1 0.6 C5 A:5BU7 1.9 51.0 1.0 C6 A:5BU7 2.9 50.7 1.0 C4 A:5BU7 2.9 52.2 1.0 H6 A:5BU7 3.0 61.0 1.0 O4 A:5BU7 3.1 52.2 1.0 OP2 A:5BU7 3.7 51.3 1.0 H5 A:U8 3.7 59.8 1.0 N7 A:A6 3.8 50.4 1.0 H3' A:A6 3.8 61.4 1.0 C8 A:A6 3.9 51.7 1.0 C5 A:A6 4.0 50.2 1.0 H2' A:A6 4.1 60.7 1.0 N1 A:5BU7 4.1 49.8 1.0 N3 A:5BU7 4.1 52.0 1.0 H8 A:A6 4.2 62.2 1.0 N9 A:A6 4.3 51.2 1.0 C4 A:A6 4.3 50.4 1.0 C5 A:U8 4.3 49.7 1.0 C6 A:A6 4.6 51.2 1.0 O5' A:5BU7 4.6 49.7 1.0 C2 A:5BU7 4.6 51.0 1.0 C3' A:A6 4.6 51.0 1.0 C2' A:A6 4.8 50.5 1.0 P A:5BU7 4.8 52.0 1.0 H62 A:A6 4.8 61.7 1.0 O4 A:U8 4.9 49.1 1.0 N6 A:A6 4.9 51.3 1.0 H3' A:5BU7 4.9 59.0 1.0 C4 A:U8 4.9 49.6 1.0 H3 A:5BU7 5.0 62.5 1.0

Bromine binding site 2 out of 4 in the Rna Dodecamer Containing A Gna A Residue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Dodecamer Containing A Gna A Residue within 5.0Å range: probe atom residue distance (Å) B Occ B:Br7 b:53.6 occ:0.58 BR B:5BU7 0.0 53.6 0.6 C5 B:5BU7 1.9 50.6 1.0 C6 B:5BU7 2.9 50.9 1.0 C4 B:5BU7 2.9 49.2 1.0 H6 B:5BU7 3.0 61.2 1.0 O4 B:5BU7 3.1 49.9 1.0 H8 B:A6 3.4 53.0 1.0 C8 B:A6 3.5 44.1 1.0 N7 B:A6 3.6 42.7 1.0 O B:HOH103 3.6 40.9 1.0 H3' B:A6 3.6 56.0 1.0 OP2 B:5BU7 3.8 51.8 1.0 N1 B:5BU7 4.1 50.6 1.0 OP2 B:A6 4.1 46.6 1.0 N3 B:5BU7 4.1 49.2 1.0 O5' B:A6 4.4 46.3 1.0 N9 B:A6 4.4 45.1 1.0 C5 B:A6 4.5 44.7 1.0 C3' B:A6 4.6 46.6 1.0 H2' B:A6 4.6 55.0 1.0 C2 B:5BU7 4.6 48.8 1.0 O5' B:5BU7 4.6 50.7 1.0 P B:5BU7 4.8 50.4 1.0 H5 B:U8 4.9 66.8 1.0 P B:A6 4.9 46.6 1.0 C4 B:A6 4.9 46.1 1.0 H3 B:5BU7 5.0 59.2 1.0

Bromine binding site 3 out of 4 in the Rna Dodecamer Containing A Gna A Residue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rna Dodecamer Containing A Gna A Residue within 5.0Å range: probe atom residue distance (Å) B Occ C:Br7 b:50.2 occ:0.72 BR C:5BU7 0.0 50.2 0.7 C5 C:5BU7 1.9 46.2 1.0 C6 C:5BU7 2.9 45.9 1.0 C4 C:5BU7 2.9 46.2 1.0 H6 C:5BU7 3.0 55.2 1.0 O4 C:5BU7 3.1 47.3 1.0 H3' C:A6 3.3 54.5 1.0 N7 C:A6 3.5 44.4 1.0 H5 C:U8 3.5 60.4 1.0 C8 C:A6 3.5 45.7 1.0 OP2 C:5BU7 3.6 46.1 1.0 H8 C:A6 3.7 55.0 1.0 C5 C:A6 3.9 44.3 1.0 H2' C:A6 3.9 53.8 1.0 N9 C:A6 4.0 45.9 1.0 O C:HOH103 4.0 45.2 1.0 N1 C:5BU7 4.1 46.0 1.0 C5 C:U8 4.1 50.2 1.0 N3 C:5BU7 4.1 45.5 1.0 C3' C:A6 4.2 45.4 1.0 C4 C:A6 4.2 46.1 1.0 O5' C:A6 4.3 47.0 1.0 O4 C:U8 4.3 53.1 1.0 OP2 C:A6 4.4 49.6 1.0 C2' C:A6 4.5 44.8 1.0 O5' C:5BU7 4.5 45.1 1.0 C4 C:U8 4.6 51.3 1.0 P C:5BU7 4.6 45.5 1.0 C2 C:5BU7 4.6 45.2 1.0 C6 C:A6 4.7 43.9 1.0 C1' C:A6 4.8 44.6 1.0 H3' C:5BU7 4.8 55.8 1.0 H62 C:A6 4.9 52.4 1.0 O3' C:A6 4.9 46.8 1.0 H3 C:5BU7 5.0 54.8 1.0

Bromine binding site 4 out of 4 in the Rna Dodecamer Containing A Gna A Residue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rna Dodecamer Containing A Gna A Residue within 5.0Å range: probe atom residue distance (Å) B Occ D:Br7 b:50.1 occ:0.61 BR D:5BU7 0.0 50.1 0.6 C5 D:5BU7 1.9 49.0 1.0 C6 D:5BU7 2.9 49.5 1.0 C4 D:5BU7 2.9 48.8 1.0 H6 D:5BU7 3.0 59.6 1.0 O4 D:5BU7 3.1 46.4 1.0 H3' D:A6 3.4 57.4 1.0 N7 D:A6 3.4 46.2 1.0 C8 D:A6 3.5 46.6 1.0 OP2 D:5BU7 3.6 47.7 1.0 H8 D:A6 3.6 56.0 1.0 OP2 D:A6 3.9 52.1 1.0 C5 D:A6 4.0 45.6 1.0 O5' D:A6 4.1 50.2 1.0 N1 D:5BU7 4.1 49.2 1.0 N3 D:5BU7 4.1 50.0 1.0 N9 D:A6 4.1 47.1 1.0 H5 D:U8 4.2 62.4 1.0 C3' D:A6 4.3 47.7 1.0 H2' D:A6 4.3 58.8 1.0 C4 D:A6 4.4 46.4 1.0 O5' D:5BU7 4.5 45.8 1.0 C2 D:5BU7 4.6 49.7 1.0 P D:5BU7 4.6 47.7 1.0 P D:A6 4.7 50.2 1.0 C2' D:A6 4.7 48.9 1.0 C6 D:A6 4.8 45.3 1.0 C5 D:U8 4.8 51.9 1.0 H62 D:A6 4.8 54.5 1.0 H3' D:5BU7 4.9 57.5 1.0 H3 D:5BU7 5.0 60.1 1.0 C1' D:A6 5.0 48.4 1.0

M.K.Schlegel, S.Matsuda, C.R.Brown, J.M.Harp, J.D.Barry, D.Berman, A.Castoreno, S.Schofield, J.Szeto, M.Manoharan, K.Charisse, M.Egli, M.A.Maier. Overcoming Gna/Rna Base-Pairing Limitations Using Isonucleotides Improves the Pharmacodynamic Activity of Esc+ Galnac-Sirnas. Nucleic Acids Res. V. 49 10851 2021.
ISSN: ESSN 1362-4962
PubMed: 34648028
DOI: 10.1093/NAR/GKAB916