Bromine in PDB 7ecj: Rna Duplex Containing C-A Base Pairs

The structure of Rna Duplex Containing C-A Base Pairs, PDB code: 7ecj was solved by J.Kondo, Y.Uchida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 3.10
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.78, 47.78, 186.215, 90, 90, 120
R / Rfree (%)	23.1 / 28.3

The binding sites of Bromine atom in the Rna Duplex Containing C-A Base Pairs (pdb code 7ecj). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Rna Duplex Containing C-A Base Pairs, PDB code: 7ecj:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Rna Duplex Containing C-A Base Pairs


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 C-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:80.5 occ:1.00 BR A:CBR6 0.0 80.5 1.0 C5 A:CBR6 1.9 44.2 1.0 C6 A:CBR6 2.8 40.9 1.0 C4 A:CBR6 2.9 51.5 1.0 N4 A:CBR6 3.1 50.6 1.0 C5 A:U5 3.5 47.8 1.0 OP2 A:CBR6 3.6 56.6 1.0 C4 A:U5 3.6 46.0 1.0 C6 A:U5 3.8 48.3 1.0 N3 A:U5 3.9 44.6 1.0 O4 A:U5 4.1 50.4 1.0 N1 A:CBR6 4.1 42.6 1.0 N1 A:U5 4.2 50.3 1.0 N3 A:CBR6 4.2 48.5 1.0 C2 A:U5 4.2 46.9 1.0 N7 A:G7 4.3 47.9 1.0 O5' A:CBR6 4.5 42.7 1.0 C3' A:U5 4.5 52.9 1.0 P A:CBR6 4.6 57.7 1.0 C2 A:CBR6 4.7 43.1 1.0 C2' A:U5 4.7 51.1 1.0 O5' A:U5 4.8 41.2 1.0 OP2 A:U5 4.9 67.4 1.0 O6 A:G7 4.9 64.8 1.0

Bromine binding site 2 out of 3 in the Rna Duplex Containing C-A Base Pairs


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 C-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:82.2 occ:1.00 BR B:CBR6 0.0 82.2 1.0 C5 B:CBR6 1.9 66.0 1.0 C6 B:CBR6 2.9 62.4 1.0 C4 B:CBR6 2.9 62.1 1.0 N4 B:CBR6 3.2 58.6 1.0 C5 B:U5 3.4 70.2 1.0 C4 B:U5 3.7 62.8 1.0 C6 B:U5 3.8 66.3 1.0 OP2 B:CBR6 4.0 62.6 1.0 O4 B:U5 4.1 57.7 1.0 N1 B:CBR6 4.2 66.6 1.0 N3 B:U5 4.2 63.3 1.0 N3 B:CBR6 4.2 50.8 1.0 N1 B:U5 4.3 64.6 1.0 C2 B:U5 4.5 66.8 1.0 C2 B:CBR6 4.7 55.0 1.0 C2' B:U5 4.9 63.7 1.0

Bromine binding site 3 out of 3 in the Rna Duplex Containing C-A Base Pairs


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rna Duplex Containing C-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:Br6 b:121.8 occ:1.00 BR C:CBR6 0.0 121.8 1.0 C5 C:CBR6 1.9 129.7 1.0 C6 C:CBR6 2.8 131.3 1.0 C4 C:CBR6 2.9 131.4 1.0 N4 C:CBR6 3.1 127.5 1.0 OP2 C:CBR6 3.6 114.5 1.0 C2 C:U5 3.7 109.3 1.0 N3 C:U5 3.8 106.9 1.0 N1 C:U5 3.9 101.1 1.0 C2' C:U5 4.0 113.7 1.0 C4 C:U5 4.1 100.2 1.0 N1 C:CBR6 4.1 139.8 1.0 C6 C:U5 4.1 98.2 1.0 O2 C:U5 4.1 117.0 1.0 N3 C:CBR6 4.2 131.6 1.0 O5' C:CBR6 4.2 117.2 1.0 C5 C:U5 4.2 97.8 1.0 C3' C:U5 4.5 110.4 1.0 C1' C:U5 4.6 103.1 1.0 P C:CBR6 4.6 118.1 1.0 C2 C:CBR6 4.7 137.2 1.0 O4 C:U5 4.7 94.8 1.0 O2' C:U5 5.0 106.2 1.0

J.Kondo, Y.Uchida. Rna Duplex Containing C-A Base Pairs To Be Published.