Atomistry » Arsenic » PDB 1b92-1fyx » 1biz
Atomistry »
  Arsenic »
    PDB 1b92-1fyx »
      1biz »

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

Protein crystallography data

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

Arsenic Binding Sites:

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 1biz

Go back to Arsenic Binding Sites List in 1biz
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 1biz

Go back to Arsenic Binding Sites List in 1biz
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 1biz

Go back to Arsenic Binding Sites List in 1biz
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 1biz

Go back to Arsenic Binding Sites List in 1biz
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

Reference:

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
Page generated: Tue Oct 27 16:46:09 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy