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Arsenic in PDB 4dmn: Hiv-1 Integrase Catalytical Core Domain

Protein crystallography data

The structure of Hiv-1 Integrase Catalytical Core Domain, PDB code: 4dmn was solved by L.Feng, M.Kvaratskhelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.44 / 2.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.082, 73.082, 64.808, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 27.6

Other elements in 4dmn:

The structure of Hiv-1 Integrase Catalytical Core Domain also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Hiv-1 Integrase Catalytical Core Domain (pdb code 4dmn). 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-1 Integrase Catalytical Core Domain, PDB code: 4dmn:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4dmn

Go back to Arsenic Binding Sites List in 4dmn
Arsenic binding site 1 out of 2 in the Hiv-1 Integrase Catalytical 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 Catalytical Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As301

b:59.5
occ:1.00
SG A:CYS65 2.2 55.0 1.0
CB A:CYS65 3.0 56.6 1.0
ND2 A:ASN120 3.2 56.2 1.0
N A:CYS65 3.5 55.9 1.0
CG A:ASN120 3.6 62.4 1.0
CD1 A:LEU74 3.7 53.1 1.0
OD1 A:ASN120 3.8 64.7 1.0
CA A:CYS65 3.8 56.2 1.0
C A:ASP64 4.1 54.9 1.0
OE1 A:GLU92 4.2 74.8 1.0
CB A:ASN120 4.5 58.7 1.0
CD A:GLU92 4.5 73.7 1.0
CA A:ASP64 4.6 54.8 1.0
OG1 A:THR97 4.7 43.7 1.0
O A:ASP64 4.7 54.5 1.0
OE2 A:GLU92 5.0 75.8 1.0

Arsenic binding site 2 out of 2 in 4dmn

Go back to Arsenic Binding Sites List in 4dmn
Arsenic binding site 2 out of 2 in the Hiv-1 Integrase Catalytical 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 Catalytical Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As302

b:60.3
occ:1.00
SG A:CYS130 2.3 52.3 1.0
CB A:CYS130 3.2 50.5 1.0
C A:LYS136 4.1 0.8 1.0
N A:GLN137 4.1 0.8 1.0
CG2 A:ILE135 4.2 80.2 1.0
CA A:LYS136 4.3 99.0 1.0
CB A:GLN137 4.4 0.9 1.0
O A:LYS136 4.5 0.9 1.0
N A:LYS136 4.5 93.0 1.0
O A:ILE135 4.5 88.9 1.0
C A:ILE135 4.5 88.2 1.0
CB A:ILE135 4.5 80.0 1.0
CA A:CYS130 4.5 50.3 1.0
CG A:GLN137 4.6 0.6 1.0
CA A:GLN137 4.7 0.0 1.0
CD2 A:PHE121 4.9 64.6 1.0
CD A:GLN137 5.0 0.6 1.0
CG A:PHE121 5.0 62.0 1.0

Reference:

J.J.Kessl, N.Jena, Y.Koh, H.Taskent-Sezgin, A.Slaughter, L.Feng, S.De Silva, L.Wu, S.F.Le Grice, A.Engelman, J.R.Fuchs, M.Kvaratskhelia. Multimode, Cooperative Mechanism of Action of Allosteric Hiv-1 Integrase Inhibitors. J.Biol.Chem. V. 287 16801 2012.
ISSN: ISSN 0021-9258
PubMed: 22437836
DOI: 10.1074/JBC.M112.354373
Page generated: Tue Oct 27 16:52:31 2020

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