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Cadmium in PDB 3vqb: Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid

Protein crystallography data

The structure of Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid, PDB code: 3vqb 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) 34.40 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.868, 63.227, 81.996, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.2

Other elements in 3vqb:

The structure of Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid also contains other interesting chemical elements:

Fluorine (F) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid (pdb code 3vqb). 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 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid, PDB code: 3vqb:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3vqb

Go back to Cadmium Binding Sites List in 3vqb
Cadmium binding site 1 out of 4 in the Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid


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 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:34.6
occ:0.82
OE1 A:GLU92 2.0 27.4 1.0
NE2 A:HIS67 2.5 30.6 1.0
SG A:CYS65 2.6 31.5 1.0
CD A:GLU92 2.9 41.6 1.0
OE2 A:GLU92 3.1 42.8 1.0
CD2 A:HIS67 3.2 34.2 1.0
CD A:CD302 3.5 38.3 1.0
CB A:CYS65 3.6 31.8 1.0
CE1 A:HIS67 3.6 33.3 1.0
CG A:GLU92 4.4 39.4 1.0
CG A:HIS67 4.5 35.1 1.0
ND1 A:HIS67 4.6 30.6 1.0
CG2 A:VAL72 4.9 36.8 1.0
CA A:CYS65 4.9 31.6 1.0

Cadmium binding site 2 out of 4 in 3vqb

Go back to Cadmium Binding Sites List in 3vqb
Cadmium binding site 2 out of 4 in the Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid


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 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:38.3
occ:1.00
OE2 A:GLU92 2.4 42.8 1.0
OD2 A:ASP116 2.5 32.5 1.0
O A:HOH426 2.5 31.0 1.0
SG A:CYS65 2.8 31.5 1.0
O A:HOH403 2.8 27.1 1.0
CG A:ASP116 3.3 31.0 1.0
CB A:CYS65 3.4 31.8 1.0
OD1 A:ASP116 3.4 28.5 1.0
CD A:GLU92 3.5 41.6 1.0
CD A:CD301 3.5 34.6 0.8
OE1 A:GLU92 4.0 27.4 1.0
O A:HOH425 4.0 43.2 1.0
O A:HOH402 4.4 35.2 1.0
N A:CYS65 4.4 30.7 1.0
CE2 A:PHE121 4.5 40.3 1.0
CA A:CYS65 4.5 31.6 1.0
OD1 A:ASN120 4.6 31.7 1.0
CG A:GLU92 4.7 39.4 1.0
CB A:ASP116 4.8 30.8 1.0

Cadmium binding site 3 out of 4 in 3vqb

Go back to Cadmium Binding Sites List in 3vqb
Cadmium binding site 3 out of 4 in the Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid


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 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:46.6
occ:1.00
OE2 B:GLU92 2.0 45.4 1.0
OD2 B:ASP116 2.1 30.6 1.0
O B:HOH415 2.6 45.0 1.0
SG B:CYS65 2.7 45.1 1.0
O B:HOH404 2.7 28.5 1.0
O B:HOH430 2.8 55.2 1.0
CD B:GLU92 3.2 44.6 1.0
CG B:ASP116 3.2 38.9 1.0
CB B:CYS65 3.5 39.9 1.0
CD B:CD302 3.6 56.5 1.0
OD1 B:ASP116 3.6 42.9 1.0
OE1 B:GLU92 3.8 26.3 1.0
CG B:GLU92 4.3 37.8 1.0
O B:HOH403 4.3 41.7 1.0
CE2 B:PHE121 4.5 41.3 1.0
N B:CYS65 4.5 35.7 1.0
CB B:ASP116 4.5 32.2 1.0
OD1 B:ASN120 4.7 54.1 1.0
CA B:CYS65 4.7 33.5 1.0
ND2 B:ASN120 4.8 40.9 1.0

Cadmium binding site 4 out of 4 in 3vqb

Go back to Cadmium Binding Sites List in 3vqb
Cadmium binding site 4 out of 4 in the Hiv-1 in Core Domain in Complex with 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid


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 6-Fluoro-4H-1,3-Benzodioxine-8- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:56.5
occ:1.00
OE1 B:GLU92 2.0 26.3 1.0
CE1 B:HIS67 2.1 48.8 1.0
O B:HOH430 2.4 55.2 1.0
O B:HOH426 2.6 25.1 1.0
SG B:CYS65 2.8 45.1 1.0
NE2 B:HIS67 2.9 58.0 1.0
CD B:GLU92 3.0 44.6 1.0
OE2 B:GLU92 3.2 45.4 1.0
ND1 B:HIS67 3.2 53.1 1.0
CD B:CD301 3.6 46.6 1.0
CB B:CYS65 3.7 39.9 1.0
O B:HOH429 4.0 58.3 1.0
CD2 B:HIS67 4.1 45.6 1.0
CG B:HIS67 4.3 46.9 1.0
CG B:GLU92 4.4 37.8 1.0
OD2 B:ASP116 4.9 30.6 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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