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Cadmium in PDB 3wnf: Cyclic Hexapeptide Ckidnc in Complex with Hiv-1 Integrase

Protein crystallography data

The structure of Cyclic Hexapeptide Ckidnc in Complex with Hiv-1 Integrase, PDB code: 3wnf 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) 43.36 / 1.45
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 50.070, 50.070, 102.570, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.2

Other elements in 3wnf:

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

Cadmium binding site 1 out of 4 in 3wnf

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

b:15.0
occ:1.00
O A:HOH1111 2.3 13.4 1.0
CL A:CL1003 2.5 15.8 1.0
OD2 A:ASP116 2.5 14.8 1.0
OE2 A:GLU92 2.5 14.7 1.0
SG A:CYS65 2.6 14.4 1.0
CG A:ASP116 3.4 14.0 1.0
CD A:GLU92 3.5 12.7 1.0
OD1 A:ASP116 3.6 13.8 1.0
CB A:CYS65 3.6 9.4 1.0
CD A:CD1002 3.7 15.7 1.0
O A:HOH1139 4.0 17.1 1.0
O A:HOH1128 4.1 20.1 1.0
OD1 A:ASN120 4.2 15.2 1.0
OE1 A:GLU92 4.2 18.0 1.0
O A:HOH1114 4.4 18.5 1.0
O A:HOH1109 4.4 17.4 1.0
CG A:GLU92 4.5 12.3 1.0
N A:CYS65 4.6 15.9 1.0
ND2 A:ASN120 4.7 14.5 1.0
CA A:CYS65 4.7 14.1 1.0
CB A:ASP116 4.7 16.8 1.0
CG A:ASN120 4.9 16.1 1.0

Cadmium binding site 2 out of 4 in 3wnf

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

b:15.7
occ:1.00
NE2 A:HIS67 2.3 14.1 1.0
OE1 A:GLU92 2.4 18.0 1.0
SG A:CYS65 2.6 14.4 1.0
OE2 A:GLU92 2.9 14.7 1.0
CD A:GLU92 3.1 12.7 1.0
CE1 A:HIS67 3.1 18.8 1.0
CD2 A:HIS67 3.3 16.1 1.0
CB A:CYS65 3.5 9.4 1.0
CD A:CD1001 3.7 15.0 1.0
ND1 A:HIS67 4.3 20.4 1.0
CG A:HIS67 4.4 15.2 1.0
CG A:GLU92 4.5 12.3 1.0
O A:HOH1133 4.6 29.2 1.0
C A:CYS65 4.7 12.1 1.0
CA A:CYS65 4.7 14.1 1.0

Cadmium binding site 3 out of 4 in 3wnf

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

b:15.6
occ:1.00
NE2 B:HIS67 2.2 15.4 1.0
OE1 B:GLU92 2.4 18.7 1.0
SG B:CYS65 2.6 15.2 1.0
OE2 B:GLU92 3.0 15.5 1.0
CD B:GLU92 3.0 13.4 1.0
CE1 B:HIS67 3.1 18.8 1.0
CD2 B:HIS67 3.3 16.9 1.0
CB B:CYS65 3.5 9.9 1.0
CD B:CD302 3.7 14.8 1.0
ND1 B:HIS67 4.3 21.1 1.0
CG B:HIS67 4.4 14.7 1.0
CG B:GLU92 4.5 12.2 1.0
O B:HOH447 4.7 26.7 1.0
C B:CYS65 4.7 13.7 1.0
CA B:CYS65 4.7 14.2 1.0

Cadmium binding site 4 out of 4 in 3wnf

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

b:14.8
occ:1.00
O B:HOH410 2.3 11.9 1.0
CL B:CL303 2.5 15.8 1.0
OD2 B:ASP116 2.5 14.8 1.0
OE2 B:GLU92 2.5 15.5 1.0
SG B:CYS65 2.6 15.2 1.0
CG B:ASP116 3.4 15.0 1.0
CD B:GLU92 3.5 13.4 1.0
OD1 B:ASP116 3.6 13.6 1.0
CB B:CYS65 3.6 9.9 1.0
CD B:CD301 3.7 15.6 1.0
O B:HOH414 4.0 16.9 1.0
O B:HOH430 4.1 21.1 1.0
OE1 B:GLU92 4.1 18.7 1.0
ND2 B:ASN120 4.2 12.8 1.0
O B:HOH417 4.4 16.8 1.0
CG B:GLU92 4.5 12.2 1.0
N B:CYS65 4.6 16.2 1.0
OD1 B:ASN120 4.7 17.1 1.0
CB B:ASP116 4.7 16.9 1.0
CA B:CYS65 4.7 14.2 1.0
CG B:ASN120 4.9 18.1 1.0
CE2 B:PHE121 5.0 19.1 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: Sat Dec 12 08:23:36 2020

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