Bromine in PDB 7bpg: Structure of Serinol Nucleic Acid - Rna Complex

The structure of Structure of Serinol Nucleic Acid - Rna Complex, PDB code: 7bpg 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 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.363, 46.918, 47.540, 90.00, 114.54, 90.00
R / Rfree (%)	23.2 / 27.1

The structure of Structure of Serinol Nucleic Acid - Rna Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Bromine atom in the Structure of Serinol Nucleic Acid - Rna Complex (pdb code 7bpg). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of Serinol Nucleic Acid - Rna Complex, PDB code: 7bpg:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of Serinol 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 Serinol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:44.2 occ:1.00 BR A:5BU6 0.0 44.2 1.0 C5 A:5BU6 1.9 39.2 1.0 C6 A:5BU6 2.8 43.5 1.0 C4 A:5BU6 2.9 39.9 1.0 O4 A:5BU6 3.1 39.8 1.0 O D:HOH201 3.5 44.2 1.0 C4 A:C5 3.5 44.4 1.0 O D:HOH207 3.5 50.7 1.0 OP2 A:5BU6 3.6 42.6 1.0 O A:HOH104 3.6 56.3 1.0 N3 D:F7U108 3.6 44.1 1.0 N3 A:C5 3.6 45.2 1.0 O A:HOH105 3.6 52.0 1.0 C5 A:C5 3.7 43.9 1.0 C2 A:C5 3.8 46.0 1.0 C4 D:F7U108 3.9 39.1 1.0 C6 A:C5 3.9 46.4 1.0 O A:HOH103 4.0 52.6 1.0 N1 A:C5 4.0 46.3 1.0 N4 A:C5 4.0 43.5 1.0 C2B D:F7U108 4.1 42.7 1.0 N1 A:5BU6 4.1 41.1 1.0 N9 D:F7U108 4.1 43.7 1.0 N3 A:5BU6 4.1 39.3 1.0 C2 D:F7U108 4.2 39.0 1.0 O2 A:C5 4.5 42.8 1.0 C2' A:C5 4.6 45.2 1.0 N2 D:F7U108 4.6 41.4 1.0 C2 A:5BU6 4.6 36.6 1.0 C3' A:C5 4.6 40.8 1.0 C5 D:F7U108 4.8 40.9 1.0 C1' A:C5 4.9 46.6 1.0 P A:5BU6 5.0 46.0 1.0

Bromine binding site 2 out of 4 in the Structure of Serinol 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 Serinol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Br6 b:51.2 occ:1.00 BR C:5BU6 0.0 51.2 1.0 C5 C:5BU6 1.9 49.3 1.0 C6 C:5BU6 2.9 47.1 1.0 C4 C:5BU6 2.9 47.6 1.0 O4 C:5BU6 3.0 41.9 1.0 C4 C:C5 3.5 47.8 1.0 C5 C:C5 3.6 51.4 1.0 N3 B:F7U108 3.6 41.7 1.0 O C:HOH105 3.7 45.2 1.0 N3 C:C5 3.7 52.0 1.0 C6 C:C5 3.7 48.9 1.0 OP2 C:5BU6 3.8 49.8 1.0 C4 B:F7U108 3.8 39.0 1.0 C2 C:C5 3.8 50.3 1.0 N1 C:C5 3.9 50.9 1.0 C2B B:F7U108 4.0 45.8 1.0 N9 B:F7U108 4.0 40.7 1.0 N4 C:C5 4.1 50.1 1.0 N1 C:5BU6 4.1 45.4 1.0 N3 C:5BU6 4.2 45.8 1.0 C2 B:F7U108 4.2 38.3 1.0 C3' C:C5 4.4 51.7 1.0 C2' C:C5 4.4 53.4 1.0 O2 C:C5 4.5 52.0 1.0 N2 B:F7U108 4.6 39.2 1.0 C2 C:5BU6 4.7 48.1 1.0 O5' C:5BU6 4.7 53.6 1.0 C1' C:C5 4.7 53.3 1.0 C5 B:F7U108 4.7 41.9 1.0 P C:5BU6 4.8 53.4 1.0 C8 B:F7U108 4.9 40.3 1.0 N1 B:F7U108 5.0 40.7 1.0

Bromine binding site 3 out of 4 in the Structure of Serinol Nucleic Acid - Rna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Serinol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Br6 b:61.3 occ:1.00 BR E:5BU6 0.0 61.3 1.0 C5 E:5BU6 1.9 54.7 1.0 C6 E:5BU6 2.8 55.5 1.0 C4 E:5BU6 2.9 53.1 1.0 O4 E:5BU6 3.1 48.9 1.0 O E:HOH105 3.3 54.4 1.0 C4 E:C5 3.5 53.9 1.0 N3 E:C5 3.5 53.7 1.0 O H:HOH203 3.6 56.9 1.0 C5 E:C5 3.6 54.2 1.0 OP2 E:5BU6 3.6 65.7 1.0 O E:HOH101 3.6 46.4 1.0 N3 H:F7U108 3.7 49.9 1.0 C2 E:C5 3.7 56.9 1.0 C6 E:C5 3.7 57.6 1.0 O H:HOH207 3.7 60.2 1.0 N1 E:C5 3.8 57.1 1.0 C4 H:F7U108 4.0 49.1 1.0 N4 E:C5 4.0 50.4 1.0 O H:HOH204 4.1 53.8 1.0 N1 E:5BU6 4.1 53.5 1.0 N3 E:5BU6 4.1 51.8 1.0 C2B H:F7U108 4.1 54.4 1.0 N9 H:F7U108 4.3 52.4 1.0 C2' E:C5 4.3 61.9 1.0 C2 H:F7U108 4.3 46.4 1.0 C3' E:C5 4.3 65.0 1.0 O2 E:C5 4.4 56.7 1.0 O5' E:5BU6 4.6 62.1 1.0 C2 E:5BU6 4.6 52.3 1.0 N2 H:F7U108 4.6 48.4 1.0 C1' E:C5 4.6 60.9 1.0 P E:5BU6 4.7 64.0 1.0 N1 F:F7X105 4.9 45.9 1.0 C5 H:F7U108 5.0 48.0 1.0

Bromine binding site 4 out of 4 in the Structure of Serinol Nucleic Acid - Rna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Serinol Nucleic Acid - Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Br6 b:52.0 occ:1.00 BR G:5BU6 0.0 52.0 1.0 C5 G:5BU6 1.9 47.9 1.0 C6 G:5BU6 2.9 50.7 1.0 C4 G:5BU6 2.9 44.6 1.0 O4 G:5BU6 3.1 43.9 1.0 O G:HOH106 3.2 47.0 1.0 C4 G:C5 3.6 46.2 1.0 O G:HOH103 3.6 49.9 1.0 N3 G:C5 3.6 46.2 1.0 N3 F:F7U108 3.6 40.6 1.0 C5 G:C5 3.7 45.7 1.0 O G:HOH105 3.7 45.9 1.0 C2 G:C5 3.7 47.3 1.0 C6 G:C5 3.8 48.2 1.0 OP2 G:5BU6 3.8 48.9 1.0 O G:HOH101 3.8 45.8 1.0 N1 G:C5 3.8 45.1 1.0 C4 F:F7U108 4.0 43.1 1.0 C2B F:F7U108 4.0 41.9 1.0 O F:HOH211 4.0 52.2 1.0 N4 G:C5 4.1 43.7 1.0 N1 G:5BU6 4.1 47.4 1.0 C3' G:C5 4.2 48.4 1.0 N3 G:5BU6 4.2 45.3 1.0 N9 F:F7U108 4.2 43.7 1.0 C2 F:F7U108 4.3 42.2 1.0 O2 G:C5 4.4 49.0 1.0 C2' G:C5 4.4 47.5 1.0 N2 F:F7U108 4.6 40.8 1.0 O5' G:5BU6 4.6 49.8 1.0 C1' G:C5 4.7 49.1 1.0 C2 G:5BU6 4.7 46.4 1.0 P G:5BU6 4.7 50.1 1.0 O3' G:C5 5.0 48.8 1.0 C5 F:F7U108 5.0 40.6 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