Bromine in PDB 7d7u: Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate

The structure of Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate, PDB code: 7d7u was solved by M.Suzuki, Y.Takahashi, J.Saito, H.Miyagi, F.Shinohara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.170, 65.770, 40.790, 105.83, 96.46, 87.56
R / Rfree (%)	20.4 / 24.7

The binding sites of Bromine atom in the Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate (pdb code 7d7u). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate, PDB code: 7d7u:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Br601 b:51.8 occ:1.00 BR8 A:8BR601 0.0 51.8 1.0 C8 A:8BR601 1.9 31.0 1.0 N7 A:8BR601 2.8 27.6 1.0 N9 A:8BR601 2.9 25.4 1.0 O4' A:8BR601 3.3 22.5 1.0 C1' A:8BR601 3.4 25.9 1.0 O A:HOH780 3.7 51.4 1.0 C2' A:8BR601 3.7 27.5 1.0 C3' A:8BR601 3.7 27.1 1.0 OH A:TYR529 3.8 23.2 1.0 CZ A:TYR529 3.8 20.5 1.0 CE1 A:TYR529 3.9 19.4 1.0 C5 A:8BR601 3.9 25.1 1.0 C4' A:8BR601 4.0 25.7 1.0 C4 A:8BR601 4.0 24.5 1.0 C5' A:8BR601 4.2 23.9 1.0 CE2 A:TYR529 4.4 20.1 1.0 CD1 A:TYR529 4.6 20.5 1.0 O5' A:8BR601 4.8 22.5 1.0 CD2 A:TYR529 5.0 20.1 1.0 O3P A:8BR601 5.0 18.1 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Br601 b:45.1 occ:1.00 BR8 B:8BR601 0.0 45.1 1.0 C8 B:8BR601 1.9 36.9 1.0 N7 B:8BR601 2.8 34.5 1.0 N9 B:8BR601 2.9 32.4 1.0 O4' B:8BR601 3.4 28.3 1.0 C1' B:8BR601 3.5 29.9 1.0 C2' B:8BR601 3.6 30.1 1.0 C3' B:8BR601 3.7 30.7 1.0 CZ B:TYR529 3.9 28.0 1.0 C4' B:8BR601 3.9 28.8 1.0 C5 B:8BR601 3.9 33.7 1.0 C5' B:8BR601 4.0 27.1 1.0 OH B:TYR529 4.0 23.1 1.0 C4 B:8BR601 4.0 31.3 1.0 CE1 B:TYR529 4.2 26.5 1.0 CE2 B:TYR529 4.2 27.5 1.0 O B:HOH735 4.2 33.7 1.0 CD1 B:TYR529 4.7 26.0 1.0 CD2 B:TYR529 4.7 24.9 1.0 CG B:TYR529 5.0 24.2 1.0 O1P B:8BR601 5.0 27.5 1.0 O2' B:8BR601 5.0 33.3 1.0

Bromine binding site 3 out of 3 in the Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of AGO2 Mid Domain in Complex with 8-Br-Adenosin-5'- Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Br601 b:83.6 occ:1.00 BR8 C:8BR601 0.0 83.6 1.0 C8 C:8BR601 1.9 59.6 1.0 N7 C:8BR601 2.8 50.3 1.0 N9 C:8BR601 2.9 55.0 1.0 O4' C:8BR601 3.3 42.2 1.0 C1' C:8BR601 3.4 47.8 1.0 CZ C:TYR529 3.5 44.2 1.0 OH C:TYR529 3.6 42.1 1.0 C2' C:8BR601 3.6 43.6 1.0 CE2 C:TYR529 3.7 43.8 1.0 C3' C:8BR601 3.8 43.1 1.0 C5 C:8BR601 3.9 53.2 1.0 C4' C:8BR601 4.0 40.8 1.0 C4 C:8BR601 4.0 54.8 1.0 CE1 C:TYR529 4.0 42.7 1.0 C5' C:8BR601 4.2 39.6 1.0 CD2 C:TYR529 4.4 43.0 1.0 O5' C:8BR601 4.4 36.1 1.0 CD1 C:TYR529 4.7 43.1 1.0 O2P C:8BR601 4.8 31.7 1.0 CG C:TYR529 4.8 42.8 1.0 O2' C:8BR601 5.0 49.6 1.0

F.Shinohara, T.Oashi, T.Harumoto, T.Nishikawa, Y.Takayama, H.Miyagi, Y.Takahashi, T.Nakajima, T.Sawada, Y.Koda, A.Makino, A.Sato, K.Hamaguch, M.Suzuki, J.Yamamoto, Y.Tomari, J.I.Saito. Sirna Potency Enhancement Via Chemical Modifications of Nucleotide Bases at the 5'-End of the Sirna Guide Strand. Rna 2020.
ISSN: ESSN 1469-9001
PubMed: 33177188
DOI: 10.1261/RNA.073783.119