Atomistry » Cadmium » PDB 3heq-3o7s » 3l3v
Atomistry »
  Cadmium »
    PDB 3heq-3o7s »
      3l3v »

Cadmium in PDB 3l3v: Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose

Protein crystallography data

The structure of Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose, PDB code: 3l3v was solved by J.Wielens, D.K.Chalmers, M.J.Scanlon, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.73 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.085, 60.714, 81.463, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose (pdb code 3l3v). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose, PDB code: 3l3v:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3l3v

Go back to Cadmium Binding Sites List in 3l3v
Cadmium binding site 1 out of 4 in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:26.3
occ:0.85
OE1 A:GLU92 2.1 22.5 1.0
O A:HOH14 2.2 22.0 1.0
NE2 A:HIS67 2.3 29.7 1.0
SG A:CYS65 2.5 33.7 1.0
CD A:GLU92 3.0 33.2 1.0
OE2 A:GLU92 3.1 35.6 1.0
CE1 A:HIS67 3.2 29.8 1.0
CD2 A:HIS67 3.4 29.9 1.0
CB A:CYS65 3.5 29.4 1.0
CD A:CD1002 3.5 34.1 1.0
CG A:GLU92 4.4 31.9 1.0
ND1 A:HIS67 4.4 32.8 1.0
CG A:HIS67 4.5 33.7 1.0
CA A:CYS65 4.8 33.6 1.0
C A:CYS65 4.8 35.1 1.0
CG1 A:VAL72 5.0 29.3 1.0

Cadmium binding site 2 out of 4 in 3l3v

Go back to Cadmium Binding Sites List in 3l3v
Cadmium binding site 2 out of 4 in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:34.1
occ:1.00
OE2 A:GLU92 2.3 35.6 1.0
OD2 A:ASP116 2.4 35.3 1.0
O A:HOH217 2.5 38.2 1.0
SG A:CYS65 2.6 33.7 1.0
O A:HOH2 2.7 27.8 1.0
CB A:CYS65 3.3 29.4 1.0
CG A:ASP116 3.3 30.9 1.0
CD A:GLU92 3.4 33.2 1.0
OD1 A:ASP116 3.4 31.5 1.0
CD A:CD1001 3.5 26.3 0.8
OE1 A:GLU92 3.9 22.5 1.0
N A:CYS65 4.3 33.1 1.0
CA A:CYS65 4.4 33.6 1.0
CG A:GLU92 4.5 31.9 1.0
OD1 A:ASN120 4.5 30.5 1.0
OD1 A:ASP64 4.6 44.0 0.8
O A:HOH213 4.6 31.5 1.0
O A:HOH14 4.6 22.0 1.0
CE2 A:PHE121 4.7 34.3 1.0
CB A:ASP116 4.7 29.6 1.0
C A:ASP64 5.0 39.6 1.0

Cadmium binding site 3 out of 4 in 3l3v

Go back to Cadmium Binding Sites List in 3l3v
Cadmium binding site 3 out of 4 in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:45.6
occ:1.00
OE2 B:GLU92 2.1 43.9 1.0
OD2 B:ASP116 2.4 43.7 1.0
SG B:CYS65 2.6 42.8 1.0
O B:HOH31 2.6 42.3 1.0
O B:HOH3 2.8 34.3 1.0
O B:HOH224 2.8 49.8 1.0
CD B:GLU92 3.3 44.6 1.0
CB B:CYS65 3.3 39.3 1.0
CG B:ASP116 3.4 47.5 1.0
CD B:CD1004 3.5 52.0 1.0
OD1 B:ASP116 3.6 42.0 1.0
OE1 B:GLU92 4.0 42.3 1.0
CG B:GLU92 4.3 40.8 1.0
N B:CYS65 4.3 39.7 1.0
OD1 B:ASN120 4.4 40.9 1.0
CA B:CYS65 4.4 37.8 1.0
CE2 B:PHE121 4.6 39.7 1.0
CB B:ASP116 4.8 38.6 1.0
O B:HOH19 4.8 50.4 1.0
ND2 B:ASN120 4.9 32.2 1.0
OD1 B:ASP64 4.9 51.9 1.0

Cadmium binding site 4 out of 4 in 3l3v

Go back to Cadmium Binding Sites List in 3l3v
Cadmium binding site 4 out of 4 in the Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Hiv-1 Integrase Core Domain in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1004

b:52.0
occ:1.00
NE2 B:HIS67 2.3 46.1 1.0
OE1 B:GLU92 2.3 42.3 1.0
SG B:CYS65 2.7 42.8 1.0
O B:HOH4 2.8 41.9 1.0
OE2 B:GLU92 2.9 43.9 1.0
O B:HOH224 2.9 49.8 1.0
CD B:GLU92 3.0 44.6 1.0
CE1 B:HIS67 3.3 50.6 1.0
CD2 B:HIS67 3.3 47.8 1.0
CB B:CYS65 3.5 39.3 1.0
CD B:CD1003 3.5 45.6 1.0
ND1 B:HIS67 4.4 46.6 1.0
O B:HOH19 4.4 50.4 1.0
CG B:GLU92 4.5 40.8 1.0
CG B:HIS67 4.5 47.5 1.0
CA B:CYS65 4.9 37.8 1.0

Reference:

J.Wielens, S.J.Headey, D.Jeevarajah, D.I.Rhodes, J.Deadman, D.K.Chalmers, M.J.Scanlon, M.W.Parker. Crystal Structure of the Hiv-1 Integrase Core Domain in Complex with Sucrose Reveals Details of An Allosteric Inhibitory Binding Site Febs Lett. V. 584 1455 2010.
ISSN: ISSN 0014-5793
PubMed: 20227411
DOI: 10.1016/J.FEBSLET.2010.03.016
Page generated: Sat Dec 12 08:22:26 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy