Lead in PDB 1y95: Hiv-1 Dis(Mal) Duplex Pb-Soaked

The structure of Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95 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)	7.97 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.200, 59.200, 65.800, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 25.3

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

Magnesium

(Mg)

10 atoms

The binding sites of Lead atom in the Hiv-1 Dis(Mal) Duplex Pb-Soaked (pdb code 1y95). This binding sites where shown within 5.0 Angstroms radius around Lead atom.
In total 3 binding sites of Lead where determined in the Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95:
Jump to Lead binding site number: 1; 2; 3;

Lead binding site 1 out of 3 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 1 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Pb36 b:57.4 occ:0.41 OP2 A:A8 2.6 59.4 1.0 N7 A:G9 2.9 55.6 1.0 O6 A:G9 3.6 57.9 1.0 C5 A:G9 3.7 55.5 1.0 C8 A:G9 3.9 54.9 1.0 C6 A:G9 4.0 56.4 1.0 P A:A8 4.0 60.0 1.0 OP2 A:G9 4.2 69.8 1.0 OP1 A:A8 4.6 58.9 1.0 N7 A:G10 4.7 52.9 1.0 C2' A:G7 4.8 55.5 1.0 O3' A:G7 4.8 59.0 1.0 C4 A:G9 4.9 54.3 1.0 C3' A:G7 4.9 56.1 1.0 N9 A:G9 4.9 54.5 1.0 O6 A:G10 4.9 54.0 1.0

Lead binding site 2 out of 3 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 2 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb31 b:79.8 occ:0.23 OP1 B:G9 2.7 52.5 0.5 OP1 A:G9 2.8 68.7 1.0 OP1 B:G9 3.4 53.2 0.5 OP2 B:G9 3.4 54.1 0.5 OP2 A:G10 3.4 62.3 1.0 O3' B:A8 3.6 52.5 0.5 P B:G9 3.6 52.7 0.5 O3' B:A8 3.7 53.3 0.5 P B:G9 3.8 51.8 0.5 P A:G9 4.2 68.2 1.0 P A:G10 4.3 62.9 1.0 OP1 A:G10 4.5 63.4 1.0 O3' A:A8 4.5 68.1 1.0 O3' A:G9 4.5 61.7 1.0 O2' B:A8 4.6 56.4 0.5 O5' B:G9 4.8 50.7 0.5 C5' B:G9 4.8 47.8 0.5 OP2 B:G9 4.8 51.8 0.5 C3' B:A8 4.9 52.9 0.5 C3' B:A8 5.0 53.2 0.5

Lead binding site 3 out of 3 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Lead with other atoms in the Pb binding site number 3 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range: probe atom residue distance (Å) B Occ B:Pb35 b:60.8 occ:0.55 OP2 B:A8 2.6 45.9 0.5 N7 B:G9 2.6 47.6 0.5 N7 B:G9 2.7 45.7 0.5 OP1 B:A8 3.2 46.6 0.5 C8 B:G9 3.4 45.4 0.5 C8 B:G9 3.6 47.5 0.5 C5 B:G9 3.6 47.1 0.5 O6 B:G9 3.6 47.3 0.5 OP2 B:G9 3.7 51.8 0.5 C5 B:G9 3.8 45.0 0.5 P B:A8 3.9 46.5 0.5 C6 B:G9 4.0 47.2 0.5 O6 B:G9 4.2 45.3 0.5 P B:A8 4.3 47.5 0.5 OP1 B:A8 4.3 46.4 0.5 OP2 B:A8 4.3 47.7 0.5 C6 B:G9 4.3 45.0 0.5 O B:HOH143 4.4 68.0 0.8 N9 B:G9 4.6 45.4 0.5 N7 B:G10 4.6 41.1 1.0 C2' B:G7 4.7 46.0 0.5 O5' B:G9 4.7 50.7 0.5 O6 B:G10 4.7 40.8 1.0 P B:G9 4.8 51.8 0.5 N9 B:G9 4.8 47.6 0.5 C4 B:G9 4.8 44.9 0.5 C4 B:G9 4.8 47.1 0.5 O3' B:G7 4.8 47.2 0.5 C3' B:G7 4.8 46.4 0.5 O5' B:A8 5.0 48.8 0.5

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