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Cadmium in PDB 3wng: Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase

Protein crystallography data

The structure of Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase, PDB code: 3wng was solved by J.Wielens, D.K.Chalmers, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.07 / 1.75
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 50.250, 50.250, 102.710, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.2

Other elements in 3wng:

The structure of Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 3wng

Go back to Cadmium Binding Sites List in 3wng
Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Pkidnp in Complex with 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 Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:18.2
occ:1.00
OE1 A:GLU92 2.1 20.7 1.0
NE2 A:HIS67 2.1 17.9 1.0
SG A:CYS65 2.5 16.8 1.0
CD A:GLU92 2.9 17.9 1.0
OE2 A:GLU92 3.0 17.5 1.0
CE1 A:HIS67 3.0 19.7 1.0
CD2 A:HIS67 3.2 19.7 1.0
CB A:CYS65 3.5 17.2 1.0
CD A:CD1002 3.8 17.2 1.0
ND1 A:HIS67 4.2 22.6 1.0
CG A:HIS67 4.3 17.9 1.0
CG A:GLU92 4.4 16.7 1.0
CA A:CYS65 4.7 15.7 1.0
C A:CYS65 4.7 14.4 1.0
O A:HOH1163 4.7 34.0 1.0
O2 A:SO41005 4.9 72.6 1.0
N A:THR66 4.9 15.3 1.0

Cadmium binding site 2 out of 4 in 3wng

Go back to Cadmium Binding Sites List in 3wng
Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Pkidnp in Complex with 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 Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:17.2
occ:1.00
O A:HOH1101 2.4 15.0 1.0
OD2 A:ASP116 2.4 18.6 1.0
OE2 A:GLU92 2.5 17.5 1.0
CL A:CL1003 2.5 16.1 1.0
SG A:CYS65 2.5 16.8 1.0
CD A:GLU92 3.3 17.9 1.0
CG A:ASP116 3.4 15.8 1.0
CB A:CYS65 3.6 17.2 1.0
OD1 A:ASP116 3.6 18.4 1.0
CD A:CD1001 3.8 18.2 1.0
OE1 A:GLU92 3.9 20.7 1.0
O A:HOH1115 3.9 19.1 1.0
O A:HOH1109 4.0 17.9 1.0
OD1 A:ASN120 4.2 20.8 1.0
CG A:GLU92 4.4 16.7 1.0
O A:HOH1102 4.4 17.0 1.0
N A:CYS65 4.5 18.1 1.0
CA A:CYS65 4.6 15.7 1.0
ND2 A:ASN120 4.7 14.9 1.0
CB A:ASP116 4.8 17.2 1.0
CG A:ASN120 4.9 16.6 1.0

Cadmium binding site 3 out of 4 in 3wng

Go back to Cadmium Binding Sites List in 3wng
Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Pkidnp in Complex with 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 Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:18.0
occ:1.00
OE1 B:GLU92 1.9 21.5 1.0
NE2 B:HIS67 2.2 17.0 1.0
SG B:CYS65 2.5 16.8 1.0
CD B:GLU92 2.9 17.1 1.0
OE2 B:GLU92 3.0 17.7 1.0
CE1 B:HIS67 3.1 19.8 1.0
CD2 B:HIS67 3.2 19.2 1.0
CB B:CYS65 3.4 17.7 1.0
CD B:CD302 3.8 17.3 1.0
ND1 B:HIS67 4.3 22.6 1.0
CG B:HIS67 4.3 17.9 1.0
CG B:GLU92 4.4 16.7 1.0
O B:HOH434 4.5 38.1 1.0
CA B:CYS65 4.7 15.9 1.0
C B:CYS65 4.7 14.7 1.0
N B:THR66 5.0 15.4 1.0

Cadmium binding site 4 out of 4 in 3wng

Go back to Cadmium Binding Sites List in 3wng
Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Pkidnp in Complex with 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 Cyclic Hexapeptide Pkidnp in Complex with Hiv-1 Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:17.3
occ:1.00
O B:HOH401 2.4 15.7 1.0
OD2 B:ASP116 2.4 18.9 1.0
OE2 B:GLU92 2.4 17.7 1.0
CL B:CL303 2.5 16.7 1.0
SG B:CYS65 2.6 16.8 1.0
CD B:GLU92 3.4 17.1 1.0
CG B:ASP116 3.4 15.7 1.0
OD1 B:ASP116 3.6 19.2 1.0
CB B:CYS65 3.6 17.7 1.0
CD B:CD301 3.8 18.0 1.0
OE1 B:GLU92 3.9 21.5 1.0
O B:HOH413 3.9 19.8 1.0
O B:HOH405 4.1 20.1 1.0
OD1 B:ASN120 4.2 19.7 1.0
CG B:GLU92 4.4 16.7 1.0
O B:HOH402 4.4 16.4 1.0
N B:CYS65 4.5 17.2 1.0
CA B:CYS65 4.6 15.9 1.0
ND2 B:ASN120 4.7 15.7 1.0
CB B:ASP116 4.8 16.9 1.0
CG B:ASN120 4.9 17.2 1.0

Reference:

S.E.Northfield, J.Wielens, S.J.Headey, M.Mulcair, M.J.Scanlon, M.W.Parker, P.E.Thompson, D.K.Chalmers. Hexapeptide Mimetics of Ledgf in Complex with Hiv-1 Integrase To Be Published.
Page generated: Sun Jan 24 09:56:20 2021

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