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Cadmium in PDB 3vq4: Fragments Bound to Hiv-1 Integrase

Protein crystallography data

The structure of Fragments Bound to Hiv-1 Integrase, PDB code: 3vq4 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) 49.63 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.601, 62.323, 82.087, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Fragments Bound to Hiv-1 Integrase (pdb code 3vq4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Fragments Bound to Hiv-1 Integrase, PDB code: 3vq4:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3vq4

Go back to Cadmium Binding Sites List in 3vq4
Cadmium binding site 1 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Fragments Bound to Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:24.7
occ:0.70
OE1 A:GLU92 1.6 20.6 1.0
NE2 A:HIS67 2.5 24.0 1.0
SG A:CYS65 2.5 25.6 1.0
CD A:GLU92 2.6 32.8 1.0
OE2 A:GLU92 2.9 38.8 1.0
CE1 A:HIS67 3.3 28.7 1.0
CB A:CYS65 3.5 28.7 1.0
CD A:CD302 3.5 32.8 1.0
CD2 A:HIS67 3.5 29.5 1.0
O A:HOH434 3.8 56.1 1.0
CG A:GLU92 4.1 32.6 1.0
ND1 A:HIS67 4.5 23.0 1.0
CG A:HIS67 4.6 27.5 1.0
CA A:CYS65 4.8 28.7 1.0
C A:CYS65 4.9 29.5 1.0
CG1 A:VAL72 5.0 27.1 1.0

Cadmium binding site 2 out of 4 in 3vq4

Go back to Cadmium Binding Sites List in 3vq4
Cadmium binding site 2 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Fragments Bound to Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:32.8
occ:1.00
OE2 A:GLU92 2.5 38.8 1.0
OD2 A:ASP116 2.5 34.1 1.0
SG A:CYS65 2.6 25.6 1.0
O A:HOH401 2.6 20.6 1.0
CG A:ASP116 3.3 24.6 1.0
OD1 A:ASP116 3.3 27.9 1.0
CB A:CYS65 3.4 28.7 1.0
CD A:CD301 3.5 24.7 0.7
CD A:GLU92 3.5 32.8 1.0
OE1 A:GLU92 3.9 20.6 1.0
N A:CYS65 4.3 30.1 1.0
CA A:CYS65 4.5 28.7 1.0
O A:HOH434 4.5 56.1 1.0
OD1 A:ASN120 4.6 25.2 1.0
O A:HOH408 4.7 31.9 1.0
CB A:ASP116 4.7 25.2 1.0
CG A:GLU92 4.8 32.6 1.0
CE2 A:PHE121 4.9 33.7 1.0

Cadmium binding site 3 out of 4 in 3vq4

Go back to Cadmium Binding Sites List in 3vq4
Cadmium binding site 3 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Fragments Bound to Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:43.6
occ:1.00
OE2 B:GLU92 2.1 39.1 1.0
OD2 B:ASP116 2.3 32.3 1.0
O B:HOH430 2.6 35.4 1.0
SG B:CYS65 2.7 36.1 1.0
O B:HOH407 2.8 23.5 1.0
CD B:GLU92 3.2 40.0 1.0
CG B:ASP116 3.3 40.4 1.0
CB B:CYS65 3.5 39.2 1.0
OD1 B:ASP116 3.5 40.9 1.0
CD B:CD302 3.6 52.2 1.0
OE1 B:GLU92 3.7 44.0 1.0
N B:CYS65 4.3 39.1 1.0
CE2 B:PHE121 4.4 35.5 1.0
CG B:GLU92 4.5 39.4 1.0
OD1 B:ASN120 4.5 37.9 1.0
CA B:CYS65 4.6 38.5 1.0
O B:HOH418 4.6 39.9 1.0
CB B:ASP116 4.6 37.9 1.0
ND2 B:ASN120 4.8 35.5 1.0
O B:HOH435 4.9 42.1 1.0

Cadmium binding site 4 out of 4 in 3vq4

Go back to Cadmium Binding Sites List in 3vq4
Cadmium binding site 4 out of 4 in the Fragments Bound to Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Fragments Bound to Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:52.2
occ:1.00
NE2 B:HIS67 2.3 45.9 1.0
OE1 B:GLU92 2.4 44.0 1.0
SG B:CYS65 2.7 36.1 1.0
O B:HOH443 2.7 39.2 1.0
CD2 B:HIS67 3.2 44.5 1.0
CD B:GLU92 3.3 40.0 1.0
CE1 B:HIS67 3.4 44.4 1.0
OE2 B:GLU92 3.5 39.1 1.0
CD B:CD301 3.6 43.6 1.0
CB B:CYS65 3.7 39.2 1.0
CG B:HIS67 4.4 44.8 1.0
ND1 B:HIS67 4.5 44.7 1.0
O B:HOH435 4.6 42.1 1.0
CG B:GLU92 4.8 39.4 1.0
CA B:CYS65 4.9 38.5 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 09:56:05 2021

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