Bromine in PDB 1y3s: Hiv-1 Dis Rna Subtype F- Mpd Form

The structure of Hiv-1 Dis Rna Subtype F- Mpd Form, PDB code: 1y3s was solved by E.Ennifar, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	27.243, 117.794, 94.587, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 26.2

The structure of Hiv-1 Dis Rna Subtype F- Mpd Form also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	3 atoms

The binding sites of Bromine atom in the Hiv-1 Dis Rna Subtype F- Mpd Form (pdb code 1y3s). 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 Rna Subtype F- Mpd Form, PDB code: 1y3s:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Hiv-1 Dis Rna Subtype F- Mpd Form


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 Rna Subtype F- Mpd Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3 b:44.5 occ:0.31 BR A:5BU3 0.0 44.5 0.3 C5 A:5BU3 1.9 43.7 1.0 C6 A:5BU3 2.8 43.9 1.0 C4 A:5BU3 2.9 45.1 1.0 O4 A:5BU3 3.2 46.2 1.0 C6 A:U2 3.5 40.7 1.0 C5 A:U2 3.5 40.7 1.0 N1 A:U2 3.7 42.0 1.0 C4 A:U2 3.7 40.2 1.0 O A:HOH40 3.8 40.1 1.0 N3 A:U2 3.8 39.9 1.0 C2 A:U2 3.9 42.0 1.0 K A:K24 3.9 49.8 0.8 OP2 A:5BU3 3.9 52.0 1.0 C3' A:U2 4.1 46.9 1.0 N1 A:5BU3 4.2 44.8 1.0 N3 A:5BU3 4.2 43.8 1.0 C2' A:U2 4.3 46.1 1.0 O4 A:U2 4.3 41.3 1.0 C1' A:U2 4.5 44.2 1.0 O5' A:5BU3 4.5 50.5 1.0 O5' A:U2 4.6 45.2 1.0 O2 A:U2 4.6 44.1 1.0 C2 A:5BU3 4.7 45.0 1.0 P A:5BU3 4.8 52.6 1.0 OP2 A:U2 4.9 43.4 1.0 O3' A:U2 5.0 51.2 1.0

Bromine binding site 2 out of 2 in the Hiv-1 Dis Rna Subtype F- Mpd Form


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 Rna Subtype F- Mpd Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Br3 b:43.0 occ:0.32 BR B:5BU3 0.0 43.0 0.3 C5 B:5BU3 1.9 38.6 1.0 C6 B:5BU3 2.8 39.4 1.0 C4 B:5BU3 2.9 39.1 1.0 O B:HOH66 3.2 43.7 1.0 O4 B:5BU3 3.2 39.7 1.0 OP2 B:5BU3 3.4 47.8 1.0 K B:K24 3.7 67.0 1.0 C6 B:U2 4.0 35.9 1.0 C5 B:U2 4.0 36.9 1.0 N1 B:5BU3 4.1 40.7 1.0 N3 B:5BU3 4.2 37.7 1.0 N1 B:U2 4.2 38.4 1.0 O5' B:5BU3 4.3 47.0 1.0 C3' B:U2 4.3 45.8 1.0 C4 B:U2 4.4 38.3 1.0 P B:5BU3 4.4 49.0 1.0 C2 B:U2 4.5 37.6 1.0 N3 B:U2 4.5 37.0 1.0 C2' B:U2 4.6 44.6 1.0 O5' B:U2 4.7 50.6 1.0 C2 B:5BU3 4.7 39.7 1.0 O3' B:U2 4.9 47.8 1.0 C1' B:U2 4.9 42.2 1.0 OP2 B:U2 4.9 51.2 1.0

E.Ennifar, P.Dumas. Polymorphism of Bulged-Out Residues in Hiv-1 Rna Dis Kissing Complex and Structure Comparison with Solution Studies. J.Mol.Biol. V. 356 771 2006.
ISSN: ISSN 0022-2836
PubMed: 16403527
DOI: 10.1016/J.JMB.2005.12.022