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Arsenic in PDB 3lpt: Hiv Integrase

Protein crystallography data

The structure of Hiv Integrase, PDB code: 3lpt was solved by S.Nicolet, F.Christ, A.Voet, A.Marchand, S.V.Strelkov, M.De Maeyer, P.Chaltin, Z.Debyzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.55 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.000, 72.000, 65.490, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 27.2

Other elements in 3lpt:

The structure of Hiv Integrase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Arsenic Binding Sites:

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

Arsenic binding site 1 out of 2 in 3lpt

Go back to Arsenic Binding Sites List in 3lpt
Arsenic binding site 1 out of 2 in the Hiv Integrase


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Hiv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As65

b:28.1
occ:0.60
AS A:CAF65 0.0 28.1 0.6
O1 A:CAF65 2.0 27.9 0.6
CE1 A:CAF65 2.0 26.0 0.6
SG A:CAF65 2.2 24.4 0.6
CB A:CAF65 3.1 24.5 0.6
OD1 A:ASN120 3.4 26.8 1.0
ND2 A:ASN120 3.5 24.5 1.0
CG A:ASN120 3.6 24.9 1.0
N A:CAF65 3.6 23.4 0.6
O A:HOH305 3.8 25.3 1.0
CA A:CAF65 3.9 24.4 0.6
O A:HOH341 4.1 39.5 1.0
CG A:GLU92 4.1 33.8 1.0
OE1 A:GLU92 4.1 39.7 1.0
C A:ASP64 4.2 23.1 1.0
OG1 A:THR97 4.5 18.1 1.0
CD A:GLU92 4.6 37.8 1.0
CB A:ASN120 4.6 22.3 1.0
O A:ASP64 4.7 22.8 1.0
O A:HOH309 4.7 25.5 1.0
CA A:ASP64 4.8 23.1 1.0
O A:HOH444 4.8 31.3 1.0

Arsenic binding site 2 out of 2 in 3lpt

Go back to Arsenic Binding Sites List in 3lpt
Arsenic binding site 2 out of 2 in the Hiv Integrase


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Hiv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As130

b:36.7
occ:1.00
AS A:CAF130 0.0 36.7 1.0
O1 A:CAF130 2.0 33.1 1.0
CE1 A:CAF130 2.0 31.9 1.0
SG A:CAF130 2.2 22.5 1.0
CB A:CAF130 3.1 17.0 1.0
O A:ILE135 4.2 20.5 1.0
CG2 A:ILE135 4.2 21.1 1.0
N A:GLN137 4.4 30.1 1.0
CA A:CAF130 4.4 16.6 1.0
C A:LYS136 4.5 27.5 1.0
O A:LYS136 4.6 25.8 1.0
C A:ILE135 4.6 21.8 1.0
CB A:ILE135 4.7 21.2 1.0
CA A:GLN137 4.7 33.3 1.0
CB A:GLN137 4.8 33.6 1.0
O A:HOH378 4.8 45.2 1.0
CD2 A:PHE121 4.9 24.9 1.0
CA A:LYS136 4.9 26.3 1.0
CG1 A:VAL126 5.0 17.4 1.0

Reference:

F.Christ, A.Voet, A.Marchand, S.Nicolet, B.A.Desimmie, D.Marchand, D.Bardiot, N.J.Van Der Veken, B.Van Remoortel, S.V.Strelkov, M.De Maeyer, P.Chaltin, Z.Debyser. Rational Design of Small-Molecule Inhibitors of the Ledgf/P75-Integrase Interaction and Hiv Replication. Nat.Chem.Biol. V. 6 442 2010.
ISSN: ISSN 1552-4450
PubMed: 20473303
DOI: 10.1038/NCHEMBIO.370
Page generated: Tue Oct 27 16:50:35 2020

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