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Cadmium in PDB 4y1c: Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain

Protein crystallography data

The structure of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain, PDB code: 4y1c was solved by J.Wielens, D.K.Chalmers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.35 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.480, 61.500, 81.440, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 29.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain (pdb code 4y1c). 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 Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain, PDB code: 4y1c:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4y1c

Go back to Cadmium Binding Sites List in 4y1c
Cadmium binding site 1 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:24.7
occ:1.00
OE1 A:GLU92 1.9 17.9 1.0
NE2 A:HIS67 2.3 17.6 1.0
SG A:CYS65 2.6 19.8 1.0
CD A:GLU92 3.0 24.1 1.0
CD2 A:HIS67 3.2 17.0 1.0
CE1 A:HIS67 3.3 18.4 1.0
CB A:CYS65 3.4 19.9 1.0
CD A:CD302 3.5 26.9 1.0
OE2 A:GLU92 3.6 23.5 1.0
CG A:GLU92 4.2 25.1 1.0
CG A:HIS67 4.4 20.6 1.0
ND1 A:HIS67 4.4 19.3 1.0
CA A:CYS65 4.7 23.1 1.0
C A:CYS65 4.9 20.9 1.0

Cadmium binding site 2 out of 4 in 4y1c

Go back to Cadmium Binding Sites List in 4y1c
Cadmium binding site 2 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:26.9
occ:1.00
OD2 A:ASP116 2.3 17.8 1.0
OE2 A:GLU92 2.4 23.5 1.0
SG A:CYS65 2.6 19.8 1.0
CG A:ASP116 3.2 18.1 1.0
CD A:GLU92 3.2 24.1 1.0
CB A:CYS65 3.2 19.9 1.0
OD1 A:ASP116 3.3 18.8 1.0
OE1 A:GLU92 3.4 17.9 1.0
CD A:CD301 3.5 24.7 1.0
N A:CYS65 4.3 27.3 1.0
CA A:CYS65 4.4 23.1 1.0
OD1 A:ASN120 4.5 17.0 1.0
CG A:GLU92 4.6 25.1 1.0
CB A:ASP116 4.7 19.1 1.0
CE2 A:PHE121 4.7 21.4 1.0
ND2 A:ASN120 4.8 16.2 1.0
CA A:GLY118 5.0 16.7 1.0

Cadmium binding site 3 out of 4 in 4y1c

Go back to Cadmium Binding Sites List in 4y1c
Cadmium binding site 3 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1001

b:39.5
occ:1.00
OE2 B:GLU92 2.0 31.6 1.0
OD2 B:ASP116 2.0 25.4 1.0
CB B:CYS65 2.9 28.8 1.0
CD B:GLU92 3.1 33.5 1.0
SG B:CYS65 3.1 41.9 1.0
CG B:ASP116 3.2 32.1 1.0
CD B:CD1002 3.4 53.6 0.9
OE1 B:GLU92 3.6 26.6 1.0
OD1 B:ASP116 3.7 32.1 1.0
CA B:CYS65 4.1 31.8 1.0
OD1 B:ASN120 4.2 31.2 1.0
N B:CYS65 4.2 32.4 1.0
CG B:GLU92 4.3 33.3 1.0
CE2 B:PHE121 4.3 32.0 1.0
ND2 B:ASN120 4.4 28.5 1.0
CB B:ASP116 4.5 31.9 1.0
CG B:ASN120 4.8 31.8 1.0

Cadmium binding site 4 out of 4 in 4y1c

Go back to Cadmium Binding Sites List in 4y1c
Cadmium binding site 4 out of 4 in the Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cyclic Hexapeptide Cyc[Ndpoppkid] in Complex with Hiv-1 Integrase Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1002

b:53.6
occ:0.90
OE1 B:GLU92 2.1 26.6 1.0
NE2 B:HIS67 2.3 48.5 1.0
SG B:CYS65 3.0 41.9 1.0
CD B:GLU92 3.0 33.5 1.0
CE1 B:HIS67 3.1 45.5 1.0
CB B:CYS65 3.2 28.8 1.0
OE2 B:GLU92 3.3 31.6 1.0
CD2 B:HIS67 3.4 47.3 1.0
CD B:CD1001 3.4 39.5 1.0
ND1 B:HIS67 4.3 44.0 1.0
CG B:GLU92 4.4 33.3 1.0
CG B:HIS67 4.5 45.9 1.0
CA B:CYS65 4.7 31.8 1.0
OD2 B:ASP116 4.9 25.4 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 08:26:00 2020

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