Bromine in PDB 2fcz: Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin

The structure of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin, PDB code: 2fcz 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)	19.17 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.125, 27.191, 106.909, 90.00, 116.72, 90.00
R / Rfree (%)	23.8 / 25.6

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

Potassium

(K)

4 atoms

The binding sites of Bromine atom in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin (pdb code 2fcz). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin, PDB code: 2fcz:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


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 Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3 b:42.2 occ:0.27 BR A:5BU3 0.0 42.2 0.3 C5 A:5BU3 1.9 40.2 1.0 C6 A:5BU3 2.8 41.5 1.0 C4 A:5BU3 2.9 41.1 1.0 O4 A:5BU3 3.2 41.5 1.0 OP2 A:5BU3 3.5 39.5 1.0 C5 A:U2 3.5 38.2 1.0 C4 A:U2 3.6 39.3 1.0 C6 A:U2 3.7 38.5 1.0 N3 A:U2 3.8 38.3 1.0 N1 A:U2 3.9 38.1 1.0 C2 A:U2 3.9 39.0 1.0 O A:HOH75 4.1 29.7 1.0 N3 A:5BU3 4.1 41.3 1.0 N1 A:5BU3 4.1 41.6 1.0 O4 A:U2 4.1 39.7 1.0 C3' A:U2 4.2 36.2 1.0 O5' A:5BU3 4.2 39.9 1.0 C2' A:U2 4.4 37.1 1.0 P A:5BU3 4.4 39.3 1.0 O2 A:U2 4.6 40.4 1.0 C2 A:5BU3 4.7 41.4 1.0 C1' A:U2 4.7 37.6 1.0 O5' A:U2 4.8 34.3 1.0 O3' A:U2 4.8 37.1 1.0

Bromine binding site 2 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


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 Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br3 b:37.6 occ:0.24 BR B:5BU3 0.0 37.6 0.2 C5 B:5BU3 1.9 36.6 1.0 C6 B:5BU3 2.8 37.2 1.0 C4 B:5BU3 2.9 37.1 1.0 O4 B:5BU3 3.2 34.4 1.0 OP2 B:5BU3 3.2 38.8 1.0 C6 B:U2 3.8 41.2 1.0 C3' B:U2 3.8 41.3 1.0 C5 B:U2 3.9 42.2 1.0 O B:HOH56 4.0 36.1 1.0 O5' B:5BU3 4.1 39.3 1.0 N1 B:U2 4.1 41.3 1.0 P B:5BU3 4.1 41.2 1.0 N1 B:5BU3 4.1 38.6 1.0 N3 B:5BU3 4.1 36.8 1.0 O5' B:U2 4.2 45.6 1.0 C2' B:U2 4.3 40.9 1.0 C4 B:U2 4.4 42.0 1.0 OP2 B:U2 4.4 47.5 1.0 O3' B:U2 4.5 39.9 1.0 C2 B:U2 4.5 41.4 1.0 N7 B:G4 4.6 37.7 1.0 N3 B:U2 4.6 41.2 1.0 C1' B:U2 4.7 41.5 1.0 C2 B:5BU3 4.7 38.4 1.0 C4' B:U2 4.9 42.4 1.0 P B:U2 5.0 47.8 1.0

Bromine binding site 3 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Br3 b:26.0 occ:0.23 BR C:5BU3 0.0 26.0 0.2 C5 C:5BU3 1.9 23.4 1.0 C6 C:5BU3 2.8 25.3 1.0 C4 C:5BU3 2.9 25.3 1.0 O4 C:5BU3 3.2 23.6 1.0 O C:HOH180 3.4 38.3 1.0 OP2 C:5BU3 3.5 29.9 1.0 O C:HOH71 3.5 34.6 1.0 C6 C:U2 3.7 28.1 1.0 C5 C:U2 3.7 27.3 1.0 O C:HOH58 4.0 33.1 1.0 N1 C:U2 4.1 27.2 1.0 C3' C:U2 4.1 29.0 1.0 C4 C:U2 4.1 29.2 1.0 N3 C:5BU3 4.1 21.2 1.0 N1 C:5BU3 4.1 25.7 1.0 O5' C:5BU3 4.3 30.7 1.0 N3 C:U2 4.4 26.6 1.0 C2 C:U2 4.4 28.9 1.0 P C:5BU3 4.4 30.6 1.0 O5' C:U2 4.5 33.5 1.0 C2' C:U2 4.5 29.2 1.0 C2 C:5BU3 4.7 25.5 1.0 OP2 C:U2 4.7 33.4 1.0 O4 C:U2 4.8 28.3 1.0 C1' C:U2 4.8 28.1 1.0 O3' C:U2 4.8 28.9 1.0

Bromine binding site 4 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Br3 b:46.8 occ:0.26 BR D:5BU3 0.0 46.8 0.3 C5 D:5BU3 1.9 46.5 1.0 C6 D:5BU3 2.8 46.1 1.0 C4 D:5BU3 2.9 46.5 1.0 O4 D:5BU3 3.1 46.9 1.0 OP2 D:5BU3 3.2 44.7 1.0 C6 D:U2 3.4 36.9 1.0 C5 D:U2 3.5 36.4 1.0 C3' D:U2 3.6 40.1 1.0 N1 D:U2 3.6 36.6 1.0 C4 D:U2 3.7 36.1 1.0 N3 D:U2 3.9 36.3 1.0 C2 D:U2 3.9 36.7 1.0 C2' D:U2 4.0 38.7 1.0 O5' D:5BU3 4.1 44.3 1.0 N3 D:5BU3 4.1 45.4 1.0 P D:5BU3 4.1 45.0 1.0 N1 D:5BU3 4.1 45.6 1.0 C1' D:U2 4.3 37.4 1.0 O4 D:U2 4.4 34.3 1.0 O3' D:U2 4.4 42.3 1.0 O D:HOH87 4.6 40.3 1.0 C4' D:U2 4.6 39.8 1.0 O2 D:U2 4.6 36.5 1.0 C2 D:5BU3 4.7 45.8 1.0 O4' D:U2 4.7 36.2 1.0 C5' D:U2 4.8 42.2 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