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Cadmium in PDB 4nyf: Hiv Integrase in Complex with Inhibitor

Protein crystallography data

The structure of Hiv Integrase in Complex with Inhibitor, PDB code: 4nyf was solved by R.Coulombe, L.Fader, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.770, 62.450, 81.320, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4nyf:

The structure of Hiv Integrase in Complex with Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 4nyf

Go back to Cadmium Binding Sites List in 4nyf
Cadmium binding site 1 out of 4 in the Hiv Integrase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hiv Integrase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:55.4
occ:1.00
O A:HOH1055 2.5 46.5 1.0
O A:HOH1037 2.7 45.8 1.0
SG A:CYS65 2.7 37.6 1.0
OD2 A:ASP116 3.0 41.8 1.0
CD A:CD303 3.6 56.4 1.0
CG A:ASP116 3.7 41.3 1.0
OE1 A:GLU92 3.7 48.5 1.0
CB A:CYS65 3.8 33.3 1.0
OD1 A:ASP116 3.8 42.1 1.0
O A:HOH1001 4.1 34.3 1.0
OD1 A:ASN120 4.2 29.7 1.0
N A:CYS65 4.4 29.4 1.0
CE2 A:PHE121 4.5 27.8 1.0
CA A:CYS65 4.7 31.7 1.0
ND2 A:ASN120 4.8 28.1 1.0
CG A:ASN120 4.9 29.6 1.0
CD A:GLU92 4.9 45.9 1.0

Cadmium binding site 2 out of 4 in 4nyf

Go back to Cadmium Binding Sites List in 4nyf
Cadmium binding site 2 out of 4 in the Hiv Integrase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hiv Integrase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:56.4
occ:1.00
SG A:CYS65 2.6 37.6 1.0
OE1 A:GLU92 2.6 48.5 1.0
NE2 A:HIS67 2.6 37.3 1.0
OE2 A:GLU92 3.1 47.8 1.0
CD A:GLU92 3.2 45.9 1.0
CD2 A:HIS67 3.3 37.1 1.0
CD A:CD302 3.6 55.4 1.0
CE1 A:HIS67 3.8 39.5 1.0
CB A:CYS65 3.8 33.3 1.0
O A:HOH1001 4.5 34.3 1.0
CG A:HIS67 4.6 36.1 1.0
CG A:GLU92 4.6 42.3 1.0
ND1 A:HIS67 4.8 37.6 1.0
O A:HOH1037 4.8 45.8 1.0

Cadmium binding site 3 out of 4 in 4nyf

Go back to Cadmium Binding Sites List in 4nyf
Cadmium binding site 3 out of 4 in the Hiv Integrase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hiv Integrase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2001

b:28.2
occ:1.00
O B:HOH2114 2.4 32.6 1.0
OD2 B:ASP116 2.4 27.1 1.0
SG B:CYS65 2.6 17.1 1.0
OE2 B:GLU92 2.9 33.2 1.0
O B:HOH2182 3.3 40.8 1.0
CG B:ASP116 3.4 23.3 1.0
CD B:CD2002 3.4 22.7 1.0
CB B:CYS65 3.5 20.7 1.0
OD1 B:ASP116 3.6 21.2 1.0
O B:HOH2128 3.8 32.7 1.0
CD B:GLU92 3.9 29.9 1.0
O B:HOH2129 4.2 27.0 1.0
OE1 B:GLU92 4.3 22.4 1.0
N B:CYS65 4.3 20.9 1.0
OD1 B:ASN120 4.4 18.2 1.0
OD1 B:ASP64 4.4 35.4 1.0
CA B:CYS65 4.5 19.2 1.0
CA B:GLY118 4.7 14.3 1.0
CB B:ASP116 4.7 19.2 1.0
C B:ASP64 4.9 18.8 1.0

Cadmium binding site 4 out of 4 in 4nyf

Go back to Cadmium Binding Sites List in 4nyf
Cadmium binding site 4 out of 4 in the Hiv Integrase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hiv Integrase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2002

b:22.7
occ:1.00
OE1 B:GLU92 2.3 22.4 1.0
NE2 B:HIS67 2.4 13.6 1.0
SG B:CYS65 2.5 17.1 1.0
CD B:GLU92 3.0 29.9 1.0
OE2 B:GLU92 3.1 33.2 1.0
CD2 B:HIS67 3.3 16.4 1.0
CD B:CD2001 3.4 28.2 1.0
CE1 B:HIS67 3.5 15.9 1.0
CB B:CYS65 3.6 20.7 1.0
CG B:GLU92 4.5 27.2 1.0
CG B:HIS67 4.5 15.5 1.0
ND1 B:HIS67 4.6 14.8 1.0
CA B:CYS65 4.9 19.2 1.0
C B:CYS65 4.9 21.2 1.0
O B:HOH2129 4.9 27.0 1.0

Reference:

L.D.Fader, E.Malenfant, M.Parisien, R.Carson, F.Bilodeau, S.Landry, M.Pesant, C.Brochu, S.Morin, C.Chabot, T.Halmos, Y.Bousquet, M.D.Bailey, S.H.Kawai, R.Coulombe, S.Laplante, A.Jakalian, P.K.Bhardwaj, D.Wernic, P.Schroeder, M.Amad, P.Edwards, M.Garneau, J.Duan, M.Cordingley, R.Bethell, S.W.Mason, M.Bos, P.Bonneau, M.A.Poupart, A.M.Faucher, B.Simoneau, C.Fenwick, C.Yoakim, Y.Tsantrizos. Discovery of Bi 224436, A Noncatalytic Site Integrase Inhibitor (Ncini) of Hiv-1. Acs Med Chem Lett V. 5 422 2014.
PubMed: 24900852
DOI: 10.1021/ML500002N
Page generated: Sat Dec 12 08:25:20 2020

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