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Cadmium in PDB 1exq: Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain

Protein crystallography data

The structure of Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain, PDB code: 1exq was solved by J.C.-H.Chen, J.Krucinski, L.J.W.Miercke, J.S.Finer-Moore, A.H.Tang, A.D.Leavitt, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.11 / 1.60
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 48.886, 48.886, 103.644, 90.00, 90.00, 120.00
R / Rfree (%) 25.3 / 27.1

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 1exq

Go back to Cadmium Binding Sites List in 1exq
Cadmium binding site 1 out of 4 in the Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:25.2
occ:1.00
NE2 A:HIS67 2.4 25.8 1.0
OE1 A:GLU92 2.4 25.3 1.0
SG A:CYS65 2.6 25.1 1.0
OE2 A:GLU92 3.0 26.0 1.0
CD A:GLU92 3.0 25.1 1.0
CD2 A:HIS67 3.3 26.7 1.0
CE1 A:HIS67 3.4 27.6 1.0
CB A:CYS65 3.4 25.0 1.0
CD A:CD1002 3.7 26.4 1.0
O A:HOH1012 4.4 34.2 1.0
ND1 A:HIS67 4.5 27.4 1.0
CG A:GLU92 4.5 24.6 1.0
CG A:HIS67 4.5 26.9 1.0
CA A:CYS65 4.8 24.9 1.0
C A:CYS65 4.9 24.9 1.0

Cadmium binding site 2 out of 4 in 1exq

Go back to Cadmium Binding Sites List in 1exq
Cadmium binding site 2 out of 4 in the Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:26.4
occ:1.00
OD2 A:ASP116 2.6 29.3 1.0
OE2 A:GLU92 2.7 26.0 1.0
O A:HOH1006 2.7 27.5 1.0
SG A:CYS65 2.7 25.1 1.0
CL A:CL501 3.1 33.0 1.0
CG A:ASP116 3.4 28.2 1.0
OD1 A:ASP116 3.6 28.9 1.0
CD A:GLU92 3.6 25.1 1.0
CB A:CYS65 3.7 25.0 1.0
CD A:CD1001 3.7 25.2 1.0
O A:HOH1007 4.1 17.0 1.0
OD1 A:ASN120 4.2 23.3 1.0
OE1 A:GLU92 4.2 25.3 1.0
O A:HOH1005 4.5 25.2 1.0
N A:CYS65 4.6 25.6 1.0
CG A:GLU92 4.6 24.6 1.0
CA A:CYS65 4.8 24.9 1.0
CB A:ASP116 4.8 28.7 1.0
ND2 A:ASN120 4.8 25.3 1.0
CG A:ASN120 4.9 25.9 1.0

Cadmium binding site 3 out of 4 in 1exq

Go back to Cadmium Binding Sites List in 1exq
Cadmium binding site 3 out of 4 in the Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:24.9
occ:1.00
NE2 B:HIS67 2.4 24.4 1.0
OE1 B:GLU92 2.4 31.3 1.0
SG B:CYS65 2.6 23.6 1.0
OE2 B:GLU92 3.0 31.2 1.0
CD B:GLU92 3.1 30.6 1.0
CD2 B:HIS67 3.3 26.0 1.0
CB B:CYS65 3.5 25.2 1.0
CE1 B:HIS67 3.5 26.7 1.0
O B:HOH1011 3.6 10.0 1.0
CD B:CD1004 3.7 25.9 1.0
CG B:HIS67 4.5 26.5 1.0
CG B:GLU92 4.5 28.8 1.0
ND1 B:HIS67 4.5 27.0 1.0
CA B:CYS65 4.8 26.1 1.0
C B:CYS65 4.8 26.7 1.0

Cadmium binding site 4 out of 4 in 1exq

Go back to Cadmium Binding Sites List in 1exq
Cadmium binding site 4 out of 4 in the Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Hiv-1 Integrase Catalytic Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1004

b:25.9
occ:1.00
OD2 B:ASP116 2.5 24.3 1.0
O B:HOH1011 2.6 10.0 1.0
OE2 B:GLU92 2.6 31.2 1.0
SG B:CYS65 2.6 23.6 1.0
O B:HOH1012 2.7 26.1 1.0
CL B:CL502 3.1 35.1 1.0
CG B:ASP116 3.4 24.1 1.0
CD B:GLU92 3.5 30.6 1.0
CB B:CYS65 3.6 25.2 1.0
CD B:CD1003 3.7 24.9 1.0
OD1 B:ASP116 3.7 25.7 1.0
O B:HOH1032 3.8 28.8 1.0
OE1 B:GLU92 4.0 31.3 1.0
OD1 B:ASN120 4.2 23.8 1.0
CG B:GLU92 4.6 28.8 1.0
O B:HOH1024 4.6 30.5 1.0
N B:CYS65 4.6 26.6 1.0
CA B:CYS65 4.7 26.1 1.0
CB B:ASP116 4.8 25.6 1.0
ND2 B:ASN120 4.9 26.0 1.0
CG B:ASN120 5.0 25.6 1.0

Reference:

J.C.Chen, J.Krucinski, L.J.Miercke, J.S.Finer-Moore, A.H.Tang, A.D.Leavitt, R.M.Stroud. Crystal Structure of the Hiv-1 Integrase Catalytic Core and C-Terminal Domains: A Model For Viral Dna Binding. Proc.Natl.Acad.Sci.Usa V. 97 8233 2000.
ISSN: ISSN 0027-8424
PubMed: 10890912
DOI: 10.1073/PNAS.150220297
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