Bromine in PDB 5lr5: N6-Methyladenine Is Accommodated in A Conventional A-U Basepair

The structure of N6-Methyladenine Is Accommodated in A Conventional A-U Basepair, PDB code: 5lr5 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)	43.71 / 2.40
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	50.470, 50.470, 108.625, 90.00, 90.00, 120.00
R / Rfree (%)	24.7 / 28.7

The binding sites of Bromine atom in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair (pdb code 5lr5). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair, PDB code: 5lr5:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of N6-Methyladenine Is Accommodated in A Conventional A-U Basepair within 5.0Å range: probe atom residue distance (Å) B Occ A:Br9 b:82.5 occ:1.00 BR A:CBV9 0.0 82.5 1.0 C5 A:CBV9 1.9 76.2 1.0 C4 A:CBV9 3.0 74.5 1.0 C6 A:CBV9 3.0 74.0 1.0 N4 A:CBV9 3.2 75.2 1.0 O2P A:CBV9 3.3 76.1 1.0 C6 A:U8 3.6 73.5 1.0 C5 A:U8 3.7 73.6 1.0 N1 A:U8 3.9 73.8 1.0 C4 A:U8 4.0 73.2 1.0 C3' A:U8 4.1 74.0 1.0 N3 A:U8 4.2 72.5 1.0 C2 A:U8 4.2 72.2 1.0 C2' A:U8 4.3 73.0 1.0 N3 A:CBV9 4.3 73.9 1.0 N1 A:CBV9 4.3 73.4 1.0 O5' A:CBV9 4.4 78.1 1.0 P A:CBV9 4.4 75.8 1.0 O5' A:U8 4.5 75.0 1.0 O4 A:U8 4.6 73.6 1.0 C1' A:U8 4.6 73.9 1.0 O3P A:CBV9 4.7 86.5 1.0 O3' A:U8 4.8 81.0 1.0 C2 A:CBV9 4.9 75.0 1.0 O2 A:U8 5.0 72.0 1.0

Bromine binding site 2 out of 4 in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of N6-Methyladenine Is Accommodated in A Conventional A-U Basepair within 5.0Å range: probe atom residue distance (Å) B Occ B:Br9 b:78.3 occ:1.00 BR B:CBV9 0.0 78.3 1.0 C5 B:CBV9 1.9 77.3 1.0 C4 B:CBV9 3.0 73.6 1.0 C6 B:CBV9 3.0 76.7 1.0 N4 B:CBV9 3.2 73.6 1.0 O1P B:CBV9 3.6 82.8 1.0 C5 B:U8 3.6 80.0 1.0 C6 B:U8 3.8 81.9 1.0 C4 B:U8 3.9 76.7 1.0 N1 B:U8 4.1 81.3 1.0 N3 B:U8 4.2 76.7 1.0 N3 B:CBV9 4.3 73.2 1.0 N1 B:CBV9 4.3 74.6 1.0 C2 B:U8 4.4 79.6 1.0 O4 B:U8 4.4 75.8 1.0 C3' B:U8 4.4 76.3 1.0 O5' B:CBV9 4.5 74.8 1.0 C2' B:U8 4.6 76.0 1.0 P B:CBV9 4.6 75.5 1.0 O2P B:CBV9 4.8 81.9 1.0 C2 B:CBV9 4.9 73.2 1.0 C1' B:U8 4.9 82.0 1.0 O5' B:U8 5.0 88.1 1.0

Bromine binding site 3 out of 4 in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of N6-Methyladenine Is Accommodated in A Conventional A-U Basepair within 5.0Å range: probe atom residue distance (Å) B Occ C:Br9 b:65.3 occ:1.00 BR C:CBV9 0.0 65.3 1.0 C5 C:CBV9 1.9 58.4 1.0 C6 C:CBV9 3.0 59.2 1.0 C4 C:CBV9 3.0 57.8 1.0 N4 C:CBV9 3.2 58.1 1.0 C6 C:U8 3.4 51.4 1.0 C5 C:U8 3.4 53.3 1.0 N1 C:U8 3.5 50.4 1.0 O3P C:CBV9 3.5 61.4 1.0 C4 C:U8 3.6 53.7 1.0 N3 C:U8 3.7 51.1 1.0 C2 C:U8 3.7 52.5 1.0 C3' C:U8 4.0 54.5 1.0 C2' C:U8 4.0 52.2 1.0 O4 C:U8 4.3 51.1 1.0 C1' C:U8 4.3 48.9 1.0 N3 C:CBV9 4.3 59.6 1.0 N1 C:CBV9 4.3 57.4 1.0 O2 C:U8 4.4 57.4 1.0 O5' C:CBV9 4.5 48.7 1.0 P C:CBV9 4.6 49.9 1.0 O5' C:U8 4.6 58.8 1.0 N4 C:C10 4.8 57.4 1.0 C5 C:C10 4.8 58.6 1.0 O3' C:U8 4.8 56.5 1.0 O4' C:U8 4.9 49.7 1.0 C2 C:CBV9 4.9 59.0 1.0 O2P C:CBV9 5.0 64.4 1.0 C4' C:U8 5.0 51.0 1.0

Bromine binding site 4 out of 4 in the N6-Methyladenine Is Accommodated in A Conventional A-U Basepair


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of N6-Methyladenine Is Accommodated in A Conventional A-U Basepair within 5.0Å range: probe atom residue distance (Å) B Occ D:Br9 b:72.6 occ:1.00 BR D:CBV9 0.0 72.6 1.0 C5 D:CBV9 1.9 65.5 1.0 C4 D:CBV9 3.0 60.9 1.0 C6 D:CBV9 3.0 63.6 1.0 N4 D:CBV9 3.2 62.6 1.0 C5 D:U8 3.6 60.2 1.0 C6 D:U8 3.7 60.0 1.0 C4 D:U8 3.9 61.3 1.0 N1 D:U8 4.0 62.5 1.0 O2P D:CBV9 4.1 57.8 1.0 N3 D:U8 4.1 64.8 1.0 C2 D:U8 4.2 66.3 1.0 C3' D:U8 4.3 65.5 1.0 N3 D:CBV9 4.3 56.3 1.0 N1 D:CBV9 4.3 59.0 1.0 C2' D:U8 4.4 60.6 1.0 O4 D:U8 4.4 59.2 1.0 N4 D:C10 4.4 53.4 1.0 O5' D:CBV9 4.4 56.9 1.0 C5 D:C10 4.5 48.6 1.0 P D:CBV9 4.7 60.6 1.0 C1' D:U8 4.8 61.4 1.0 O5' D:U8 4.8 62.9 1.0 C2 D:CBV9 4.9 54.5 1.0 C4 D:C10 4.9 48.1 1.0 O1P D:CBV9 4.9 63.7 1.0 O2 D:U8 5.0 69.4 1.0 O3' D:U8 5.0 68.1 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