Bromine in PDB 1y90: Hiv-1 Dis(Mal) Duplex Mn-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Mn-Soaked, PDB code: 1y90 was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.08
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.080, 59.080, 63.659, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 24.4

The structure of Hiv-1 Dis(Mal) Duplex Mn-Soaked also contains other interesting chemical elements:

Manganese

(Mn)

12 atoms

The binding sites of Bromine atom in the Hiv-1 Dis(Mal) Duplex Mn-Soaked (pdb code 1y90). 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(Mal) Duplex Mn-Soaked, PDB code: 1y90:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


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(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:57.5 occ:0.70 BR A:5BU2 0.0 57.5 0.7 C5 A:5BU2 2.1 51.1 1.0 C4 A:5BU2 3.0 51.5 1.0 C6 A:5BU2 3.0 51.0 1.0 O4 A:5BU2 3.2 50.5 1.0 C6 A:C1 3.4 45.6 1.0 C5 A:C1 3.6 44.5 1.0 OP2 A:5BU2 3.7 49.3 1.0 N1 A:C1 3.7 46.3 1.0 C3' A:C1 3.8 47.3 1.0 C2' A:C1 4.0 46.8 1.0 C4 A:C1 4.0 45.3 1.0 C2 A:C1 4.2 46.4 1.0 O5' A:C1 4.3 48.8 1.0 N3 A:5BU2 4.3 50.6 1.0 C1' A:C1 4.3 46.1 1.0 N3 A:C1 4.3 45.9 1.0 N1 A:5BU2 4.3 50.0 1.0 O5' A:5BU2 4.4 47.0 1.0 O4 A:U3 4.4 56.4 1.0 P A:5BU2 4.5 49.6 1.0 O3' A:C1 4.6 48.3 1.0 O4' A:C1 4.6 45.7 1.0 C4' A:C1 4.7 46.7 1.0 C5 A:U3 4.8 55.0 1.0 N4 A:C1 4.8 45.5 1.0 C4 A:U3 4.8 55.3 1.0 C2 A:5BU2 4.9 50.0 1.0 C5' A:C1 5.0 47.4 1.0 O2 A:C1 5.0 44.5 1.0

Bromine binding site 2 out of 2 in the Hiv-1 Dis(Mal) Duplex Mn-Soaked


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(Mal) Duplex Mn-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:62.8 occ:0.70 BR B:5BU2 0.0 62.8 0.7 C5 B:5BU2 2.1 54.2 1.0 C6 B:5BU2 3.0 52.4 1.0 C4 B:5BU2 3.1 53.5 1.0 O4 B:5BU2 3.3 52.1 1.0 C5 B:C1 3.5 44.5 1.0 C6 B:C1 3.5 43.3 1.0 OP2 B:5BU2 3.7 47.7 1.0 C4 B:C1 3.9 44.1 1.0 N1 B:C1 3.9 43.7 1.0 C3' B:C1 4.1 44.6 1.0 O4 B:U3 4.1 45.0 1.0 N3 B:C1 4.2 43.4 1.0 C2 B:C1 4.2 44.3 1.0 N3 B:5BU2 4.3 51.5 1.0 N1 B:5BU2 4.3 49.0 1.0 C2' B:C1 4.4 44.5 1.0 O5' B:5BU2 4.4 47.4 1.0 N4 B:C1 4.5 43.5 1.0 MN B:MN104 4.6 51.7 0.5 P B:5BU2 4.6 48.1 1.0 C1' B:C1 4.7 44.9 1.0 C4 B:U3 4.7 42.3 1.0 C5 B:U3 4.7 40.3 1.0 O5' B:C1 4.8 49.0 1.0 O3' B:C1 4.9 44.7 1.0 C2 B:5BU2 4.9 51.2 1.0

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350