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Cadmium in PDB 3wne: Cyclic Hexapeptide Pkidng in Complex with Hiv-1 Integrase

Protein crystallography data

The structure of Cyclic Hexapeptide Pkidng in Complex with Hiv-1 Integrase, PDB code: 3wne 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) 39.70 / 1.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 49.680, 49.680, 102.930, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 22.8

Other elements in 3wne:

The structure of Cyclic Hexapeptide Pkidng 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 Pkidng in Complex with Hiv-1 Integrase (pdb code 3wne). 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 Pkidng in Complex with Hiv-1 Integrase, PDB code: 3wne:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3wne

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

b:23.9
occ:1.00
OE1 A:GLU92 2.1 22.7 1.0
NE2 A:HIS67 2.2 22.2 1.0
SG A:CYS65 2.6 25.6 1.0
CD A:GLU92 2.8 24.7 1.0
OE2 A:GLU92 3.0 27.5 1.0
CD2 A:HIS67 3.1 23.9 1.0
CE1 A:HIS67 3.2 26.4 1.0
CB A:CYS65 3.3 26.3 1.0
CD A:CD1002 3.8 24.0 1.0
CG A:GLU92 4.2 23.1 1.0
ND1 A:HIS67 4.3 27.4 1.0
CG A:HIS67 4.3 23.0 1.0
CA A:CYS65 4.6 23.7 1.0
C A:CYS65 4.6 23.0 1.0
O A:CYS65 5.0 23.2 1.0
N A:THR66 5.0 23.6 1.0

Cadmium binding site 2 out of 4 in 3wne

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

b:24.0
occ:1.00
O A:HOH1134 2.4 23.7 1.0
OD2 A:ASP116 2.4 28.0 1.0
CL A:CL1003 2.5 23.3 1.0
SG A:CYS65 2.5 25.6 1.0
OE2 A:GLU92 2.7 27.5 1.0
CG A:ASP116 3.4 24.6 1.0
CB A:CYS65 3.6 26.3 1.0
CD A:GLU92 3.6 24.7 1.0
OD1 A:ASP116 3.7 24.9 1.0
CD A:CD1001 3.8 23.9 1.0
O A:HOH1125 3.9 26.8 1.0
O A:HOH1118 4.1 24.8 1.0
OD1 A:ASN120 4.2 24.5 1.0
OE1 A:GLU92 4.2 22.7 1.0
O A:HOH1128 4.4 26.1 1.0
N A:CYS65 4.4 24.5 1.0
CG A:GLU92 4.5 23.1 1.0
O A:HOH1149 4.6 32.0 1.0
CA A:CYS65 4.6 23.7 1.0
ND2 A:ASN120 4.7 22.1 1.0
CB A:ASP116 4.8 23.6 1.0
CG A:ASN120 4.9 24.6 1.0
CE2 A:PHE121 5.0 24.7 1.0

Cadmium binding site 3 out of 4 in 3wne

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

b:24.0
occ:1.00
OE1 B:GLU92 2.1 21.9 1.0
NE2 B:HIS67 2.2 22.2 1.0
SG B:CYS65 2.6 24.6 1.0
CD B:GLU92 2.9 28.2 1.0
OE2 B:GLU92 3.1 30.3 1.0
CE1 B:HIS67 3.1 27.5 1.0
CD2 B:HIS67 3.2 22.4 1.0
CB B:CYS65 3.4 26.9 1.0
O B:HOH419 3.7 20.3 1.0
CD B:CD302 3.7 24.2 1.0
ND1 B:HIS67 4.3 28.0 1.0
CG B:GLU92 4.3 24.0 1.0
CG B:HIS67 4.4 22.2 1.0
CA B:CYS65 4.6 24.1 1.0
C B:CYS65 4.7 23.7 1.0
O B:HOH437 4.8 41.0 1.0

Cadmium binding site 4 out of 4 in 3wne

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

b:24.2
occ:1.00
O B:HOH419 2.3 20.3 1.0
O B:HOH420 2.3 21.1 1.0
OD2 B:ASP116 2.5 26.3 1.0
CL B:CL303 2.5 24.4 1.0
OE2 B:GLU92 2.5 30.3 1.0
SG B:CYS65 2.6 24.6 1.0
CG B:ASP116 3.4 25.1 1.0
CD B:GLU92 3.5 28.2 1.0
CB B:CYS65 3.6 26.9 1.0
OD1 B:ASP116 3.6 24.0 1.0
CD B:CD301 3.7 24.0 1.0
O B:HOH417 3.9 27.4 1.0
OE1 B:GLU92 4.1 21.9 1.0
OD1 B:ASN120 4.2 26.3 1.0
O B:HOH426 4.4 25.8 1.0
CG B:GLU92 4.5 24.0 1.0
O B:HOH439 4.5 31.2 1.0
N B:CYS65 4.5 24.8 1.0
CA B:CYS65 4.7 24.1 1.0
CB B:ASP116 4.8 24.9 1.0
ND2 B:ASN120 4.8 20.6 1.0
CG B:ASN120 4.9 25.0 1.0
CE2 B:PHE121 4.9 26.1 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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