Bromine in PDB 2fcy: Hiv-1 Dis Kissing-Loop in Complex with Neomycin

The structure of Hiv-1 Dis Kissing-Loop in Complex with Neomycin, PDB code: 2fcy was solved by E.Ennifar, J.C.Paillart, R.Marquet, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.22 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.105, 113.702, 96.165, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 25.3

The structure of Hiv-1 Dis Kissing-Loop in Complex with Neomycin also contains other interesting chemical elements:

Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Bromine atom in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin (pdb code 2fcy). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin, PDB code: 2fcy:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Hiv-1 Dis Kissing-Loop in Complex with Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3 b:41.0 occ:0.36 BR A:5BU3 0.0 41.0 0.4 C5 A:5BU3 1.9 36.8 1.0 C6 A:5BU3 2.8 36.3 1.0 C4 A:5BU3 2.9 35.2 1.0 O4 A:5BU3 3.2 35.0 1.0 OP2 A:5BU3 3.4 40.7 1.0 K A:K1004 3.8 55.0 1.0 C6 A:U2 3.8 33.6 1.0 C5 A:U2 3.9 32.4 1.0 C3' A:U2 4.1 37.3 1.0 N1 A:5BU3 4.2 36.6 1.0 N3 A:5BU3 4.2 33.8 1.0 N1 A:U2 4.3 34.2 1.0 O5' A:5BU3 4.3 38.7 1.0 O5' A:U2 4.4 40.6 1.0 P A:5BU3 4.4 39.1 1.0 C4 A:U2 4.4 32.8 1.0 OP2 A:U2 4.4 41.6 1.0 C2' A:U2 4.5 37.3 1.0 N7 A:G4 4.5 28.9 1.0 C2 A:5BU3 4.7 34.1 1.0 C2 A:U2 4.8 32.6 1.0 N3 A:U2 4.8 32.6 1.0 O3' A:U2 4.8 38.2 1.0 C1' A:U2 4.9 35.7 1.0

Bromine binding site 2 out of 2 in the Hiv-1 Dis Kissing-Loop in Complex with Neomycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Hiv-1 Dis Kissing-Loop in Complex with Neomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br3 b:29.6 occ:0.40 BR B:5BU3 0.0 29.6 0.4 C5 B:5BU3 1.9 25.1 1.0 C6 B:5BU3 2.8 26.5 1.0 C4 B:5BU3 2.9 25.5 1.0 O4 B:5BU3 3.2 24.5 1.0 C5 B:U2 3.5 32.5 1.0 O B:HOH2026 3.5 45.9 1.0 OP2 B:5BU3 3.6 36.9 1.0 C6 B:U2 3.6 30.7 1.0 O B:HOH2022 3.6 33.4 1.0 C4 B:U2 3.7 30.6 1.0 K B:K2003 3.7 49.7 1.0 N3 B:U2 3.9 30.6 1.0 N1 B:U2 4.0 31.8 1.0 O B:HOH2030 4.1 36.9 1.0 C2 B:U2 4.1 31.2 1.0 N1 B:5BU3 4.2 28.0 1.0 N3 B:5BU3 4.2 24.3 1.0 O4 B:U2 4.3 31.1 1.0 C3' B:U2 4.3 32.5 1.0 O5' B:5BU3 4.4 33.4 1.0 O B:HOH2027 4.4 51.7 1.0 C2' B:U2 4.6 32.6 1.0 P B:5BU3 4.6 34.7 1.0 C2 B:5BU3 4.7 27.8 1.0 O5' B:U2 4.7 32.4 1.0 C1' B:U2 4.8 31.8 1.0 O2 B:U2 4.9 32.0 1.0 O3' B:U2 5.0 33.4 1.0

E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.-M.Weibel, A.-M.Aubertin, P.Pale, P.Dumas, R.Marquet. Targeting the Dimerization Initiation Site of Hiv-1 Rna with Aminoglycosides: From Crystal to Cell. Nucleic Acids Res. V. 34 2328 2006.
ISSN: ISSN 0305-1048
PubMed: 16679451
DOI: 10.1093/NAR/GKL317