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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: Fri Aug 28 13:47:38 2020
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