Bromine in PDB 7bpf: Structure of L-Threoninol Nucleic Acid - Rna Complex

The structure of Structure of L-Threoninol Nucleic Acid - Rna Complex, PDB code: 7bpf was solved by Y.Kamiya, T.Satoh, A.Kodama, T.Suzuki, S.Uchiyama, K.Kato, H.Asanuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.75
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.996, 33.344, 54.055, 90.00, 115.64, 90.00
R / Rfree (%)	26.9 / 28.8

The binding sites of Bromine atom in the Structure of L-Threoninol Nucleic Acid - Rna Complex (pdb code 7bpf). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Structure of L-Threoninol Nucleic Acid - Rna Complex, PDB code: 7bpf:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Structure of L-Threoninol Nucleic Acid - Rna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of L-Threoninol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:44.7 occ:1.00 BR A:5BU6 0.0 44.7 1.0 C5 A:5BU6 1.9 38.9 1.0 C6 A:5BU6 2.9 42.0 1.0 C4 A:5BU6 2.9 38.5 1.0 O4 A:5BU6 3.1 39.7 1.0 C4 A:C5 3.4 44.1 1.0 N3 A:C5 3.5 41.8 1.0 C5 A:C5 3.5 41.6 1.0 N3 D:GT3108 3.6 34.0 1.0 O A:HOH102 3.7 39.0 1.0 C2 A:C5 3.7 44.4 1.0 C6 A:C5 3.7 43.0 1.0 OP2 A:5BU6 3.8 46.4 1.0 N1 A:C5 3.8 45.6 1.0 O D:HOH202 3.8 41.9 1.0 O D:HOH204 3.8 44.8 1.0 C2B D:GT3108 3.9 33.8 1.0 N4 A:C5 3.9 42.7 1.0 C4 D:GT3108 4.0 35.5 1.0 N1 A:5BU6 4.1 43.6 1.0 N3 A:5BU6 4.1 40.6 1.0 N9 D:GT3108 4.2 35.0 1.0 C2 D:GT3108 4.3 36.0 1.0 O2 A:C5 4.4 49.9 1.0 C3' A:C5 4.5 48.4 1.0 C2' A:C5 4.5 48.6 1.0 N2 D:GT3108 4.6 34.2 1.0 C2 A:5BU6 4.6 40.1 1.0 C1' A:C5 4.7 47.4 1.0 C2A D:GT3108 4.9 37.4 1.0 P A:5BU6 4.9 51.1 1.0 N1 C:F73105 4.9 36.8 1.0 O5' A:5BU6 4.9 49.1 1.0 C5 D:GT3108 5.0 35.9 1.0

Bromine binding site 2 out of 2 in the Structure of L-Threoninol Nucleic Acid - Rna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of L-Threoninol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:50.6 occ:1.00 BR B:5BU6 0.0 50.6 1.0 C5 B:5BU6 1.9 44.5 1.0 C6 B:5BU6 2.9 44.1 1.0 C4 B:5BU6 2.9 44.3 1.0 O4 B:5BU6 3.1 40.3 1.0 C4 B:C5 3.6 39.9 1.0 O B:HOH103 3.6 47.6 1.0 OP2 B:5BU6 3.6 50.9 1.0 N3 C:GT3108 3.6 38.8 1.0 C5 B:C5 3.6 38.1 1.0 N3 B:C5 3.7 38.0 1.0 C6 B:C5 3.7 39.2 1.0 C2 B:C5 3.7 39.1 1.0 N1 B:C5 3.8 38.0 1.0 O C:HOH206 4.0 51.3 1.0 C4 C:GT3108 4.1 42.7 1.0 N1 B:5BU6 4.2 45.5 1.0 N3 B:5BU6 4.2 44.2 1.0 C2 C:GT3108 4.2 39.1 1.0 N4 B:C5 4.2 38.8 1.0 C2B C:GT3108 4.3 44.8 1.0 C3' B:C5 4.3 45.3 1.0 C2' B:C5 4.3 41.8 1.0 N2 C:GT3108 4.3 39.9 1.0 O2 B:C5 4.4 40.1 1.0 N9 C:GT3108 4.4 43.8 1.0 O5' B:5BU6 4.6 45.6 1.0 C1' B:C5 4.6 41.0 1.0 C2 B:5BU6 4.6 43.9 1.0 P B:5BU6 4.7 48.3 1.0 O3' B:C5 5.0 48.0 1.0

Y.Kamiya, T.Satoh, A.Kodama, T.Suzuki, K.Murayama, H.Kashida, S.Uchiyama, K.Kato, H.Asanuma. Intrastrand Backbone-Nucleobase Interactions Stabilize Unwound Right-Handed Helical Structures of Heteroduplexes of L-Atna/Rna and Sna/Rna Commun Chem 2020.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-020-00400-2