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Cadmium in PDB 3vqa: Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide

Protein crystallography data

The structure of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide, PDB code: 3vqa was solved by J.Wielens, D.K.Chalmers, M.W.Parker, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.873, 61.023, 81.917, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide (pdb code 3vqa). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide, PDB code: 3vqa:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3vqa

Go back to Cadmium Binding Sites List in 3vqa
Cadmium binding site 1 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:20.6
occ:0.80
OE1 A:GLU92 2.0 18.8 1.0
SG A:CYS65 2.5 28.2 1.0
NE2 A:HIS67 2.5 24.6 1.0
CD A:GLU92 3.1 35.4 1.0
CD2 A:HIS67 3.1 24.7 1.0
CB A:CYS65 3.5 20.4 1.0
CD A:CD302 3.5 29.8 1.0
OE2 A:GLU92 3.5 37.6 1.0
CE1 A:HIS67 3.6 23.2 1.0
CG A:GLU92 4.4 34.4 1.0
CG A:HIS67 4.4 23.9 1.0
ND1 A:HIS67 4.6 24.3 1.0
CA A:CYS65 4.8 21.2 1.0
C A:CYS65 4.9 21.5 1.0

Cadmium binding site 2 out of 4 in 3vqa

Go back to Cadmium Binding Sites List in 3vqa
Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:29.8
occ:1.00
O A:HOH428 2.2 28.4 1.0
OD2 A:ASP116 2.4 29.2 1.0
SG A:CYS65 2.7 28.2 1.0
OE2 A:GLU92 2.9 37.6 1.0
CG A:ASP116 3.3 23.9 1.0
OD1 A:ASP116 3.3 26.6 1.0
CB A:CYS65 3.4 20.4 1.0
CD A:CD301 3.5 20.6 0.8
CD A:GLU92 3.7 35.4 1.0
OE1 A:GLU92 3.8 18.8 1.0
N A:CYS65 4.5 22.1 1.0
CA A:CYS65 4.6 21.2 1.0
OD1 A:ASN120 4.6 26.8 1.0
OD1 A:ASP64 4.7 54.1 1.0
CB A:ASP116 4.7 23.0 1.0
O A:HOH429 4.8 24.0 1.0
CE2 A:PHE121 4.8 30.3 1.0

Cadmium binding site 3 out of 4 in 3vqa

Go back to Cadmium Binding Sites List in 3vqa
Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:36.8
occ:1.00
OD2 B:ASP116 2.2 25.0 1.0
OE2 B:GLU92 2.3 34.9 1.0
O B:HOH433 2.6 19.6 1.0
O B:HOH441 2.6 30.3 1.0
SG B:CYS65 2.7 34.6 1.0
O B:HOH426 2.7 30.3 1.0
CD B:GLU92 3.2 31.8 1.0
CG B:ASP116 3.2 30.5 1.0
CB B:CYS65 3.4 32.0 1.0
OE1 B:GLU92 3.4 23.1 1.0
CD B:CD302 3.5 39.4 1.0
OD1 B:ASP116 3.6 29.6 1.0
N B:CYS65 4.3 31.2 1.0
OD1 B:ASN120 4.4 36.7 1.0
O B:HOH435 4.4 32.0 1.0
CA B:CYS65 4.5 30.1 1.0
CG B:GLU92 4.6 28.2 1.0
CB B:ASP116 4.6 32.5 1.0
ND2 B:ASN120 4.8 32.6 1.0
CE2 B:PHE121 4.9 27.8 1.0
O B:HOH434 4.9 34.9 1.0

Cadmium binding site 4 out of 4 in 3vqa

Go back to Cadmium Binding Sites List in 3vqa
Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv-1 in Core Domain in Complex with 1-Benzothiophen-6-Amine 1,1- Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:39.4
occ:1.00
O B:HOH435 2.0 32.0 1.0
NE2 B:HIS67 2.3 36.9 1.0
OE1 B:GLU92 2.5 23.1 1.0
O B:HOH426 2.5 30.3 1.0
SG B:CYS65 2.6 34.6 1.0
O B:HOH434 2.7 34.9 1.0
CD2 B:HIS67 3.2 36.6 1.0
CE1 B:HIS67 3.2 41.1 1.0
CD B:CD301 3.5 36.8 1.0
CD B:GLU92 3.5 31.8 1.0
CB B:CYS65 3.6 32.0 1.0
OE2 B:GLU92 3.9 34.9 1.0
ND1 B:HIS67 4.4 38.5 1.0
CG B:HIS67 4.4 38.6 1.0
CG B:GLU92 4.8 28.2 1.0
CA B:CYS65 4.9 30.1 1.0
OD2 B:ASP116 5.0 25.0 1.0

Reference:

J.Wielens, S.J.Headey, D.I.Rhodes, R.J.Mulder, O.Dolezal, J.J.Deadman, J.Newman, D.K.Chalmers, M.W.Parker, T.S.Peat, M.J.Scanlon. Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification? J Biomol Screen V. 18 147 2013.
ISSN: ISSN 1087-0571
PubMed: 23139382
DOI: 10.1177/1087057112465979
Page generated: Sun Jan 24 09:56:16 2021

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