Bromine in PDB 5v1k: Structure of R-Gna Dodecamer

The structure of Structure of R-Gna Dodecamer, PDB code: 5v1k was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	23.681, 27.680, 29.050, 73.00, 87.17, 66.58
R / Rfree (%)	22.4 / 16.8

The binding sites of Bromine atom in the Structure of R-Gna Dodecamer (pdb code 5v1k). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Structure of R-Gna Dodecamer, PDB code: 5v1k:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Structure of R-Gna Dodecamer


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of R-Gna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Br107 b:21.4 occ:0.46 BR A:5BU107 0.0 21.4 0.5 BR A:5BU107 1.0 20.9 0.5 C5 A:5BU107 1.6 18.9 0.5 C5 A:5BU107 2.5 15.3 0.5 C6 A:5BU107 2.6 16.8 0.5 C4 A:5BU107 2.7 20.1 0.5 O4 A:5BU107 3.0 23.9 0.5 OP2 A:A106 3.0 20.4 1.0 C4 A:5BU107 3.3 16.1 0.5 O4 A:5BU107 3.4 17.1 0.5 C6 A:5BU107 3.5 14.4 0.5 O5' A:A106 3.5 20.5 1.0 O A:HOH224 3.5 23.8 1.0 OP2 A:5BU107 3.6 19.4 0.5 C8 A:A106 3.6 18.2 1.0 OP2 A:5BU107 3.7 16.3 0.5 P A:A106 3.8 19.3 1.0 N7 A:A106 3.9 20.0 1.0 N3 A:5BU107 3.9 17.4 0.5 N1 A:5BU107 3.9 15.4 0.5 O A:HOH205 4.1 20.6 1.0 C3' A:A106 4.3 18.1 1.0 O A:HOH204 4.4 39.8 1.0 C2 A:5BU107 4.5 17.1 0.5 O5' A:5BU107 4.5 18.9 0.5 P A:5BU107 4.5 19.6 0.5 N9 A:A106 4.6 18.0 1.0 N3 A:5BU107 4.7 14.7 0.5 C5' A:A106 4.7 19.8 1.0 OP1 A:A106 4.7 21.7 1.0 N1 A:5BU107 4.8 13.3 0.5 P A:5BU107 4.9 16.8 0.5 C5 A:A106 4.9 19.7 1.0 O3' A:A106 4.9 18.9 1.0 C4' A:A106 5.0 20.4 1.0 O5' A:5BU107 5.0 17.0 0.5 O A:HOH220 5.0 71.2 1.0

Bromine binding site 2 out of 3 in the Structure of R-Gna Dodecamer


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of R-Gna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Br107 b:20.9 occ:0.54 BR A:5BU107 0.0 20.9 0.5 C5 A:5BU107 0.9 18.9 0.5 BR A:5BU107 1.0 21.4 0.5 C5 A:5BU107 1.6 15.3 0.5 C6 A:5BU107 1.8 16.8 0.5 C4 A:5BU107 2.2 20.1 0.5 C6 A:5BU107 2.6 14.4 0.5 C4 A:5BU107 2.7 16.1 0.5 O4 A:5BU107 2.9 23.9 0.5 N1 A:5BU107 3.0 15.4 0.5 O4 A:5BU107 3.1 17.1 0.5 N3 A:5BU107 3.3 17.4 0.5 OP2 A:5BU107 3.4 16.3 0.5 OP2 A:5BU107 3.6 19.4 0.5 C2 A:5BU107 3.7 17.1 0.5 C8 A:A106 3.7 18.2 1.0 N7 A:A106 3.8 20.0 1.0 N1 A:5BU107 3.9 13.3 0.5 OP2 A:A106 3.9 20.4 1.0 N3 A:5BU107 3.9 14.7 0.5 O5' A:5BU107 4.0 18.9 0.5 O5' A:A106 4.1 20.5 1.0 O A:HOH224 4.2 23.8 1.0 C3' A:A106 4.2 18.1 1.0 C1' A:5BU107 4.2 16.2 0.5 O A:HOH205 4.3 20.6 1.0 P A:5BU107 4.3 19.6 0.5 O5' A:5BU107 4.4 17.0 0.5 O A:HOH204 4.4 39.8 1.0 P A:5BU107 4.5 16.8 0.5 N9 A:A106 4.5 18.0 1.0 O4' A:5BU107 4.5 18.5 0.5 C2 A:5BU107 4.5 15.0 0.5 P A:A106 4.6 19.3 1.0 C3' A:5BU107 4.7 19.9 0.5 C5 A:A106 4.7 19.7 1.0 O3' A:A106 4.8 18.9 1.0 C2' A:5BU107 4.8 17.4 0.5 O2 A:5BU107 4.9 18.1 0.5 C2' A:A106 4.9 18.6 1.0 C4' A:5BU107 5.0 19.2 0.5

Bromine binding site 3 out of 3 in the Structure of R-Gna Dodecamer


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of R-Gna Dodecamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Br207 b:16.5 occ:1.00 BR B:5BU207 0.0 16.5 1.0 C5 B:5BU207 1.7 12.8 1.0 C6 B:5BU207 2.7 12.3 1.0 C4 B:5BU207 2.8 12.5 1.0 OP2 B:A206 3.1 15.2 1.0 O4 B:5BU207 3.1 13.8 1.0 C8 B:A206 3.4 13.6 1.0 O B:HOH336 3.5 19.8 1.0 O5' B:A206 3.5 13.0 1.0 N7 B:A206 3.6 13.4 1.0 O A:HOH203 3.7 19.6 1.0 O B:HOH322 3.8 16.7 1.0 OP2 B:5BU207 3.9 17.5 1.0 O6 A:G104 3.9 13.0 1.0 P B:A206 4.0 13.7 1.0 O B:HOH343 4.0 31.3 1.0 O B:HOH361 4.0 29.9 1.0 N1 B:5BU207 4.0 12.8 1.0 N3 B:5BU207 4.0 12.4 1.0 O A:HOH237 4.2 18.1 1.0 C3' B:A206 4.3 14.8 1.0 N9 B:A206 4.3 13.3 1.0 O B:HOH307 4.3 21.0 0.5 C5 B:A206 4.6 14.4 1.0 C2 B:5BU207 4.6 12.8 1.0 C5' B:A206 4.8 14.0 1.0 C6 A:G104 4.8 11.5 1.0 C2' B:A206 4.8 15.0 1.0 O5' B:5BU207 4.9 14.4 1.0 P B:5BU207 4.9 17.0 1.0 OP1 B:A206 4.9 16.0 1.0 C4' B:A206 4.9 14.0 1.0 C4 B:A206 5.0 14.5 1.0

M.K.Schlegel, D.J.Foster, A.V.Kel'in, I.Zlatev, A.Bisbe, M.Jayaraman, J.G.Lackey, K.G.Rajeev, K.Charisse, J.Harp, P.S.Pallan, M.A.Maier, M.Egli, M.Manoharan. Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on Sirna. J. Am. Chem. Soc. 2017.
ISSN: ESSN 1520-5126
PubMed: 28570818
DOI: 10.1021/JACS.7B02694