Bromine in PDB 5lr4: Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6, PDB code: 5lr4 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.26 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.870, 49.870, 123.735, 90.00, 90.00, 90.00
R / Rfree (%)	26.9 / 28.9

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Bromine atom in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 (pdb code 5lr4). 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 Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6, PDB code: 5lr4:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:43.7 occ:1.00 BR A:CBV2 0.0 43.7 1.0 C5 A:CBV2 1.9 41.3 1.0 HN41 A:CBV2 2.6 46.5 1.0 C6 A:CBV2 2.9 40.1 1.0 C4 A:CBV2 2.9 38.7 1.0 H6 A:CBV2 3.0 48.2 1.0 N4 A:CBV2 3.1 38.8 1.0 H3' A:G1 3.3 44.1 1.0 N7 A:G1 3.5 33.5 1.0 C5 A:G1 3.5 32.2 1.0 O3P A:CBV2 3.6 41.6 1.0 C8 A:G1 3.7 33.7 1.0 O A:HOH202 3.7 49.2 1.0 C4 A:G1 3.8 32.5 1.0 N9 A:G1 3.8 33.2 1.0 H2' A:G1 3.9 42.0 1.0 NA A:NA101 4.0 56.9 1.0 C6 A:G1 4.0 32.3 1.0 H8 A:G1 4.1 40.5 1.0 O1P A:CBV2 4.1 42.9 1.0 N1 A:CBV2 4.1 38.0 1.0 HN42 A:CBV2 4.1 46.5 1.0 N3 A:CBV2 4.2 37.0 1.0 C3' A:G1 4.2 36.7 1.0 O5' A:G1 4.4 42.0 1.0 C2' A:G1 4.4 34.9 1.0 N3 A:G1 4.5 33.0 1.0 O5' A:CBV2 4.5 40.6 1.0 O6 A:G1 4.5 32.4 1.0 N1 A:G1 4.6 32.3 1.0 C2 A:CBV2 4.6 37.2 1.0 H5 A:C3 4.6 35.2 1.0 P A:CBV2 4.7 42.2 1.0 C1' A:G1 4.7 35.0 1.0 HO5' A:G1 4.8 50.4 1.0 H41 A:C3 4.8 35.4 1.0 C2 A:G1 4.8 32.2 1.0 O3' A:G1 4.9 40.5 1.0

Bromine binding site 2 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:45.6 occ:1.00 BR B:CBV2 0.0 45.6 1.0 C5 B:CBV2 1.9 46.3 1.0 HN42 B:CBV2 2.7 57.3 1.0 C6 B:CBV2 2.8 45.0 1.0 H6 B:CBV2 2.9 54.1 1.0 C4 B:CBV2 2.9 46.7 1.0 H3' B:G1 3.2 45.8 1.0 N4 B:CBV2 3.2 47.7 1.0 O B:HOH115 3.4 45.2 1.0 O1P B:CBV2 3.5 39.9 1.0 H2' B:G1 3.7 44.9 1.0 C5 B:G1 3.7 38.9 1.0 N7 B:G1 3.7 39.4 1.0 O B:HOH109 3.7 47.2 1.0 C4 B:G1 3.8 39.6 1.0 C8 B:G1 3.8 39.1 1.0 N9 B:G1 3.8 38.5 1.0 HO5' B:G1 3.9 47.0 1.0 C3' B:G1 4.0 38.1 1.0 N1 B:CBV2 4.1 43.6 1.0 N3 B:CBV2 4.2 46.3 1.0 HN41 B:CBV2 4.2 57.3 1.0 H8 B:G1 4.2 47.0 1.0 C2' B:G1 4.2 37.4 1.0 C6 B:G1 4.2 40.2 1.0 O5' B:CBV2 4.3 38.9 1.0 H5 B:C3 4.4 51.2 1.0 N3 B:G1 4.4 39.1 1.0 O5' B:G1 4.5 39.1 1.0 P B:CBV2 4.5 39.4 1.0 H41 B:C3 4.5 53.1 1.0 C1' B:G1 4.6 37.2 1.0 C2 B:CBV2 4.6 45.1 1.0 N1 B:G1 4.7 40.3 1.0 O3' B:G1 4.7 42.0 1.0 C2 B:G1 4.8 39.5 1.0 O6 B:G1 4.8 41.1 1.0 H3' B:CBV2 4.9 48.6 1.0

Bromine binding site 3 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br2 b:48.5 occ:1.00 BR C:CBV2 0.0 48.5 1.0 C5 C:CBV2 1.9 43.1 1.0 HN42 C:CBV2 2.6 49.4 1.0 C6 C:CBV2 2.9 40.8 1.0 C4 C:CBV2 2.9 40.3 1.0 H6 C:CBV2 3.0 49.0 1.0 N4 C:CBV2 3.1 41.1 1.0 H3' C:G1 3.3 48.2 1.0 O1P C:CBV2 3.5 45.8 1.0 N7 C:G1 3.6 43.0 1.0 C5 C:G1 3.7 38.4 1.0 NA C:NA102 3.8 56.9 1.0 C8 C:G1 3.8 40.9 1.0 HO5' C:G1 3.8 55.5 1.0 C4 C:G1 3.9 37.0 1.0 N9 C:G1 4.0 38.4 1.0 H2' C:G1 4.0 44.2 1.0 HN41 C:CBV2 4.1 49.4 1.0 N1 C:CBV2 4.1 37.2 1.0 C3' C:G1 4.2 40.4 1.0 N3 C:CBV2 4.2 38.2 1.0 C6 C:G1 4.2 37.3 1.0 H8 C:G1 4.2 49.2 1.0 O5' C:G1 4.3 46.5 1.0 O5' C:CBV2 4.3 38.9 1.0 P C:CBV2 4.5 42.5 1.0 H5 C:C3 4.5 44.3 1.0 C2' C:G1 4.5 37.1 1.0 N3 C:G1 4.6 34.1 1.0 O2P C:CBV2 4.7 45.9 1.0 C2 C:CBV2 4.7 36.2 1.0 O6 C:G1 4.7 41.2 1.0 N1 C:G1 4.7 34.7 1.0 H41 C:C3 4.8 47.3 1.0 C1' C:G1 4.8 37.5 1.0 O3' C:G1 4.8 42.3 1.0 C2 C:G1 4.9 33.9 1.0

Bromine binding site 4 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br2 b:40.2 occ:1.00 BR D:CBV2 0.0 40.2 1.0 C5 D:CBV2 1.9 36.3 1.0 HN42 D:CBV2 2.7 43.2 1.0 C6 D:CBV2 2.9 35.4 1.0 C4 D:CBV2 2.9 34.7 1.0 H6 D:CBV2 3.0 42.5 1.0 N4 D:CBV2 3.2 36.0 1.0 H3' D:G1 3.2 43.8 1.0 O1P D:CBV2 3.6 48.0 1.0 C5 D:G1 3.6 28.6 1.0 N7 D:G1 3.6 25.5 1.0 H2' D:G1 3.7 38.9 1.0 C4 D:G1 3.8 27.7 1.0 C8 D:G1 3.8 30.0 1.0 N9 D:G1 3.9 29.6 1.0 O2P D:CBV2 3.9 45.2 1.0 N1 D:CBV2 4.1 34.2 1.0 C3' D:G1 4.1 36.4 1.0 C6 D:G1 4.1 28.2 1.0 O D:HOH214 4.1 61.6 1.0 HN41 D:CBV2 4.2 43.2 1.0 N3 D:CBV2 4.2 34.2 1.0 H8 D:G1 4.2 36.1 1.0 C2' D:G1 4.3 32.4 1.0 H5 D:C3 4.3 46.5 1.0 H41 D:C3 4.3 46.4 1.0 O5' D:CBV2 4.4 41.9 1.0 N3 D:G1 4.4 26.7 1.0 P D:CBV2 4.5 42.2 1.0 O5' D:G1 4.5 40.1 1.0 C2 D:CBV2 4.6 34.2 1.0 O6 D:G1 4.6 26.1 1.0 N1 D:G1 4.7 23.7 1.0 C1' D:G1 4.7 31.4 1.0 C2 D:G1 4.7 22.4 1.0 O3' D:G1 4.8 40.5 1.0 N4 D:C3 5.0 38.6 1.0 HO5' D:G1 5.0 48.2 1.0 C5 D:C3 5.0 38.7 1.0

L.Huang, S.Ashraf, J.Wang, D.M.Lilley. Control of Box C/D Snornp Assembly By N(6)-Methylation of Adenine. Embo Rep. V. 18 1631 2017.
ISSN: ESSN 1469-3178
PubMed: 28623187
DOI: 10.15252/EMBR.201743967