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Cadmium in PDB 3ao1: Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase

Protein crystallography data

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase, PDB code: 3ao1 was solved by J.Wielens, M.W.Parker, D.K.Chalmers, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.40 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.587, 61.997, 81.765, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase (pdb code 3ao1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase, PDB code: 3ao1:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3ao1

Go back to Cadmium Binding Sites List in 3ao1
Cadmium binding site 1 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in 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 Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:36.2
occ:1.00
OE2 A:GLU92 1.9 25.7 1.0
NE2 A:HIS67 2.4 31.2 1.0
SG A:CYS65 2.6 29.0 1.0
CD A:GLU92 2.8 35.4 1.0
OE1 A:GLU92 3.0 37.4 1.0
CD2 A:HIS67 3.3 32.9 1.0
CE1 A:HIS67 3.4 33.5 1.0
CB A:CYS65 3.5 33.4 1.0
CD A:CD1004 3.5 36.8 1.0
CG A:GLU92 4.2 33.7 1.0
CG A:HIS67 4.5 32.9 1.0
ND1 A:HIS67 4.5 31.8 1.0
CA A:CYS65 4.8 33.1 1.0
C A:CYS65 5.0 34.3 1.0

Cadmium binding site 2 out of 4 in 3ao1

Go back to Cadmium Binding Sites List in 3ao1
Cadmium binding site 2 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in 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 Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:36.8
occ:1.00
OD2 A:ASP116 2.4 37.3 1.0
OE1 A:GLU92 2.4 37.4 1.0
O A:HOH30 2.5 36.6 1.0
SG A:CYS65 2.6 29.0 1.0
O A:HOH4 2.7 28.0 1.0
CB A:CYS65 3.3 33.4 1.0
CG A:ASP116 3.3 35.1 1.0
CD A:GLU92 3.5 35.4 1.0
CD A:CD1003 3.5 36.2 1.0
OD1 A:ASP116 3.5 35.0 1.0
O A:HOH220 3.8 42.2 1.0
OE2 A:GLU92 4.0 25.7 1.0
N A:CYS65 4.3 34.5 1.0
CA A:CYS65 4.4 33.1 1.0
OD1 A:ASN120 4.7 34.1 1.0
CB A:ASP116 4.7 34.2 1.0
O A:HOH16 4.8 35.2 1.0
CE2 A:PHE121 4.8 35.4 1.0
CG A:GLU92 4.8 33.7 1.0

Cadmium binding site 3 out of 4 in 3ao1

Go back to Cadmium Binding Sites List in 3ao1
Cadmium binding site 3 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in 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 Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1001

b:48.2
occ:1.00
OE2 B:GLU92 2.0 44.0 1.0
OD2 B:ASP116 2.2 38.6 1.0
O B:HOH3 2.6 43.9 1.0
SG B:CYS65 2.7 39.2 1.0
O B:HOH213 2.8 33.0 1.0
CD B:GLU92 3.1 47.7 1.0
CG B:ASP116 3.2 45.6 1.0
CB B:CYS65 3.5 44.3 1.0
OD1 B:ASP116 3.5 45.3 1.0
CD B:CD1002 3.5 55.8 1.0
OE1 B:GLU92 3.7 40.9 1.0
CG B:GLU92 4.4 45.2 1.0
N B:CYS65 4.4 40.8 1.0
O B:HOH2 4.5 43.5 1.0
CA B:CYS65 4.6 40.1 1.0
CE2 B:PHE121 4.6 42.8 1.0
CB B:ASP116 4.6 42.6 1.0
OD1 B:ASN120 4.6 46.0 1.0
ND2 B:ASN120 4.8 41.8 1.0

Cadmium binding site 4 out of 4 in 3ao1

Go back to Cadmium Binding Sites List in 3ao1
Cadmium binding site 4 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in 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 Fragment-Based Approach to the Design of Ligands Targeting A Novel Site in Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1002

b:55.8
occ:1.00
NE2 B:HIS67 2.2 49.6 1.0
OE1 B:GLU92 2.3 40.9 1.0
SG B:CYS65 2.6 39.2 1.0
O B:HOH224 2.8 40.7 1.0
CD2 B:HIS67 3.1 48.2 1.0
CD B:GLU92 3.2 47.7 1.0
CE1 B:HIS67 3.3 50.5 1.0
OE2 B:GLU92 3.4 44.0 1.0
CD B:CD1001 3.5 48.2 1.0
CB B:CYS65 3.6 44.3 1.0
CG B:HIS67 4.3 49.7 1.0
ND1 B:HIS67 4.3 49.2 1.0
CG B:GLU92 4.6 45.2 1.0
CA B:CYS65 4.9 40.1 1.0

Reference:

J.Wielens, S.J.Headey, J.J.Deadman, D.I.Rhodes, M.W.Parker, D.K.Chalmers, M.J.Scanlon. Fragment-Based Design of Ligands Targeting A Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus 1 Chemmedchem V. 6 258 2011.
ISSN: ISSN 1860-7179
PubMed: 21275048
DOI: 10.1002/CMDC.201000483
Page generated: Thu Jul 10 12:19:46 2025

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