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Cadmium in PDB 3ao4: Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase

Protein crystallography data

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase, PDB code: 3ao4 was solved by J.Wielens, S.J.Headey, 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) 38.72 / 1.95
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 48.200, 48.200, 103.600, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 25.3

Other elements in 3ao4:

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase (pdb code 3ao4). 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 on Hiv-1 Integrase, PDB code: 3ao4:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3ao4

Go back to Cadmium Binding Sites List in 3ao4
Cadmium binding site 1 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:31.0
occ:1.00
OE1 A:GLU92 1.6 22.1 1.0
NE2 A:HIS67 2.4 34.5 1.0
SG A:CYS65 2.4 27.7 1.0
CD A:GLU92 2.6 30.5 1.0
OE2 A:GLU92 2.8 34.4 1.0
CB A:CYS65 3.2 28.1 1.0
CD2 A:HIS67 3.3 31.7 1.0
CE1 A:HIS67 3.4 37.2 1.0
CD A:CD1002 3.6 32.6 1.0
O A:HOH6 3.7 26.4 1.0
CG A:GLU92 4.1 30.9 1.0
CG A:HIS67 4.5 36.5 1.0
ND1 A:HIS67 4.5 35.5 1.0
CA A:CYS65 4.6 24.1 1.0
C A:CYS65 4.8 27.9 1.0
CB A:GLU92 4.8 31.9 1.0
CG1 A:VAL72 4.9 28.0 1.0

Cadmium binding site 2 out of 4 in 3ao4

Go back to Cadmium Binding Sites List in 3ao4
Cadmium binding site 2 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:32.6
occ:1.00
OD2 A:ASP116 2.3 30.6 1.0
OE2 A:GLU92 2.3 34.4 1.0
O A:HOH19 2.4 29.1 1.0
O A:HOH6 2.4 26.4 1.0
CL A:CL501 2.5 30.7 1.0
SG A:CYS65 2.6 27.7 1.0
CD A:GLU92 3.3 30.5 1.0
CG A:ASP116 3.3 33.3 1.0
CB A:CYS65 3.5 28.1 1.0
OD1 A:ASP116 3.6 34.4 1.0
CD A:CD1001 3.6 31.0 1.0
OE1 A:GLU92 3.8 22.1 1.0
OD1 A:ASN120 4.2 29.2 1.0
CG A:GLU92 4.3 30.9 1.0
O A:HOH18 4.3 29.1 1.0
N A:CYS65 4.4 27.0 1.0
O A:HOH8 4.5 31.4 1.0
ND2 A:ASN120 4.6 30.3 1.0
CA A:CYS65 4.6 24.1 1.0
CB A:ASP116 4.7 33.2 1.0
CG A:ASN120 4.8 27.1 1.0

Cadmium binding site 3 out of 4 in 3ao4

Go back to Cadmium Binding Sites List in 3ao4
Cadmium binding site 3 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:30.8
occ:1.00
OE1 B:GLU92 1.6 25.6 1.0
NE2 B:HIS67 2.3 37.1 1.0
SG B:CYS65 2.4 29.2 1.0
CD B:GLU92 2.6 30.6 1.0
OE2 B:GLU92 2.8 35.9 1.0
CB B:CYS65 3.2 27.8 1.0
CE1 B:HIS67 3.2 36.7 1.0
CD2 B:HIS67 3.3 37.8 1.0
O B:HOH31 3.6 28.9 1.0
CD B:CD1004 3.6 32.2 1.0
CG B:GLU92 4.1 31.5 1.0
ND1 B:HIS67 4.3 36.4 1.0
CG B:HIS67 4.4 38.2 1.0
CA B:CYS65 4.5 25.4 1.0
C B:CYS65 4.8 28.6 1.0
CB B:GLU92 4.9 30.6 1.0
CG2 B:VAL72 4.9 27.0 1.0

Cadmium binding site 4 out of 4 in 3ao4

Go back to Cadmium Binding Sites List in 3ao4
Cadmium binding site 4 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on 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 on Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1004

b:32.2
occ:1.00
OE2 B:GLU92 2.3 35.9 1.0
OD2 B:ASP116 2.3 34.7 1.0
O B:HOH31 2.4 28.9 1.0
O B:HOH45 2.4 28.3 1.0
CL B:CL502 2.5 29.9 1.0
SG B:CYS65 2.6 29.2 1.0
CD B:GLU92 3.3 30.6 1.0
CG B:ASP116 3.4 33.6 1.0
CB B:CYS65 3.5 27.8 1.0
OD1 B:ASP116 3.6 34.5 1.0
CD B:CD1003 3.6 30.8 1.0
O B:HOH16 3.9 24.6 1.0
OE1 B:GLU92 3.9 25.6 1.0
OD1 B:ASN120 4.1 27.2 1.0
O B:HOH10 4.2 27.7 1.0
CG B:GLU92 4.3 31.5 1.0
N B:CYS65 4.4 26.4 1.0
ND2 B:ASN120 4.5 25.6 1.0
CA B:CYS65 4.6 25.4 1.0
O B:HOH20 4.6 32.4 1.0
CG B:ASN120 4.7 25.9 1.0
CB B:ASP116 4.7 32.6 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: Sat Dec 12 08:19:06 2020

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