Arsenic in PDB 1biz: Hiv-1 Integrase Core Domain

The structure of Hiv-1 Integrase Core Domain, PDB code: 1biz was solved by Y.Goldgur, F.Dyda, A.B.Hickman, T.M.Jenkins, R.Craigie, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.840, 71.340, 91.880, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.3

The binding sites of Arsenic atom in the Hiv-1 Integrase Core Domain (pdb code 1biz). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Hiv-1 Integrase Core Domain, PDB code: 1biz:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:As213 b:40.3 occ:1.00 SG A:CYS65 2.2 39.6 1.0 CB A:CYS65 3.0 39.2 1.0 OD1 A:ASN120 3.4 53.5 1.0 N A:CYS65 3.5 36.2 1.0 OE1 A:GLU92 3.5 51.0 1.0 CG A:ASN120 3.7 49.2 1.0 ND2 A:ASN120 3.8 47.4 1.0 CA A:CYS65 3.8 37.8 1.0 C A:ASP64 3.8 35.2 1.0 CD A:GLU92 4.2 46.9 1.0 CA A:ASP64 4.3 35.0 1.0 O A:ASP64 4.4 33.8 1.0 CD1 A:LEU74 4.4 27.8 1.0 CG A:GLU92 4.5 36.1 1.0 CB A:ASN120 4.6 42.2 1.0 O A:HOH1030 4.7 29.9 1.0 O A:HOH1036 4.8 45.9 1.0 OG1 A:THR97 4.8 18.9 1.0 CB A:GLU92 4.9 36.3 1.0

Arsenic binding site 2 out of 4 in the Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:As214 b:26.5 occ:1.00 SG A:CYS130 2.2 25.1 1.0 CB A:CYS130 3.0 24.4 1.0 C A:LYS136 3.9 22.7 1.0 N A:GLN137 3.9 24.5 1.0 CG2 A:ILE135 4.0 20.1 1.0 CA A:LYS136 4.1 21.3 1.0 O A:ILE135 4.1 19.7 1.0 C A:ILE135 4.2 19.6 1.0 N A:LYS136 4.2 19.5 1.0 O A:LYS136 4.2 22.4 1.0 CB A:ILE135 4.3 19.4 1.0 CA A:CYS130 4.4 21.4 1.0 O A:HOH1619 4.5 42.4 1.0 CA A:GLN137 4.5 26.1 1.0 O A:HOH1493 4.5 29.6 1.0 CB A:GLN137 4.8 17.5 1.0 O A:HOH1492 4.9 54.9 1.0 CA A:ILE135 5.0 19.1 1.0

Arsenic binding site 3 out of 4 in the Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:As213 b:28.9 occ:1.00 SG B:CYS65 2.4 28.1 1.0 CB B:CYS65 3.0 27.8 1.0 O B:HOH1253 3.2 43.6 1.0 N B:CYS65 3.5 23.4 1.0 ND2 B:ASN120 3.5 24.2 1.0 OD1 B:ASN120 3.6 25.8 1.0 CG B:ASN120 3.6 33.7 1.0 CA B:CYS65 3.8 26.6 1.0 C B:ASP64 3.9 22.6 1.0 CD1 B:LEU74 4.0 25.5 1.0 O B:HOH1015 4.1 38.9 1.0 CA B:ASP64 4.4 21.9 1.0 CD B:GLU92 4.5 36.1 1.0 O B:ASP64 4.5 23.7 1.0 CB B:ASN120 4.5 33.7 1.0 OE1 B:GLU92 4.6 47.7 1.0 OE2 B:GLU92 4.6 46.2 1.0 O B:HOH1076 4.7 31.2 1.0 OG1 B:THR97 4.7 14.3 1.0 CG B:GLU92 4.8 30.2 1.0

Arsenic binding site 4 out of 4 in the Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Hiv-1 Integrase Core Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:As214 b:27.2 occ:1.00 SG B:CYS130 2.0 26.6 1.0 CB B:CYS130 3.0 26.3 1.0 CB B:GLN137 3.8 43.3 1.0 O B:ILE135 3.9 24.2 1.0 C B:LYS136 4.1 35.7 1.0 N B:GLN137 4.2 40.1 1.0 O B:LYS136 4.3 34.1 1.0 CG2 B:ILE135 4.3 23.4 1.0 O B:HOH1107 4.3 42.9 1.0 C B:ILE135 4.3 25.2 1.0 CA B:CYS130 4.4 25.7 1.0 CB B:ILE135 4.5 22.6 1.0 CA B:LYS136 4.5 33.4 1.0 CA B:GLN137 4.6 43.2 1.0 N B:LYS136 4.6 29.4 1.0 CG B:GLN137 4.8 54.2 1.0

Y.Goldgur, F.Dyda, A.B.Hickman, T.M.Jenkins, R.Craigie, D.R.Davies. Three New Structures of the Core Domain of Hiv-1 Integrase: An Active Site That Binds Magnesium. Proc.Natl.Acad.Sci.Usa V. 95 9150 1998.
ISSN: ISSN 0027-8424
PubMed: 9689049
DOI: 10.1073/PNAS.95.16.9150