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Cadmium in PDB 1vsj: Asv Integrase Core Domain with Cd(II) Cofactors

Protein crystallography data

The structure of Asv Integrase Core Domain with Cd(II) Cofactors, PDB code: 1vsj was solved by G.Bujacz, J.Alexandratos, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.330, 66.330, 80.920, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Asv Integrase Core Domain with Cd(II) Cofactors (pdb code 1vsj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Asv Integrase Core Domain with Cd(II) Cofactors, PDB code: 1vsj:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1vsj

Go back to Cadmium Binding Sites List in 1vsj
Cadmium binding site 1 out of 2 in the Asv Integrase Core Domain with Cd(II) Cofactors


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Asv Integrase Core Domain with Cd(II) Cofactors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd280

b:21.5
occ:1.00
O A:HOH284 2.1 22.9 1.0
O A:HOH281 2.3 18.0 1.0
OD2 A:ASP121 2.3 27.2 1.0
OD1 A:ASP64 2.4 2.0 1.0
O A:HOH283 2.6 24.4 1.0
O A:HOH282 2.9 37.1 1.0
CG A:ASP121 3.3 23.6 1.0
CG A:ASP64 3.3 11.7 1.0
OD2 A:ASP64 3.6 18.9 1.0
OD1 A:ASP121 3.6 18.1 1.0
O A:HOH405 3.8 21.8 1.0
O A:HOH308 4.0 14.6 1.0
CD A:CD290 4.1 34.9 0.5
O A:HOH414 4.3 50.5 1.0
O A:PHE65 4.3 4.8 1.0
O A:HOH398 4.4 38.4 1.0
O A:HOH292 4.5 6.5 0.5
N A:PHE65 4.6 6.9 1.0
CB A:ASP121 4.6 21.3 1.0
CB A:ASP64 4.7 7.0 1.0

Cadmium binding site 2 out of 2 in 1vsj

Go back to Cadmium Binding Sites List in 1vsj
Cadmium binding site 2 out of 2 in the Asv Integrase Core Domain with Cd(II) Cofactors


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Asv Integrase Core Domain with Cd(II) Cofactors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd290

b:34.9
occ:0.45
O A:HOH283 2.0 24.4 1.0
OD2 A:ASP64 2.3 18.9 1.0
OE1 A:GLU157 2.5 39.6 1.0
O A:HOH292 2.7 6.5 0.5
OE2 A:GLU157 2.7 42.0 1.0
CD A:GLU157 2.9 39.4 1.0
CG A:ASP64 3.5 11.7 1.0
O A:HOH291 3.6 45.2 0.5
ND2 A:ASN160 3.7 13.1 1.0
OD1 A:ASP64 4.0 2.0 1.0
CD A:CD280 4.1 21.5 1.0
O A:HOH405 4.2 21.8 1.0
O A:PHE65 4.3 4.8 1.0
O A:HOH414 4.4 50.5 1.0
CG A:GLU157 4.4 32.2 1.0
O A:HOH307 4.5 45.8 1.0
O A:HOH281 4.5 18.0 1.0
CB A:ASP64 4.6 7.0 1.0
O A:HOH332 4.8 50.4 1.0

Reference:

G.Bujacz, J.Alexandratos, A.Wlodawer, G.Merkel, M.Andrake, R.A.Katz, A.M.Skalka. Binding of Different Divalent Cations to the Active Site of Avian Sarcoma Virus Integrase and Their Effects on Enzymatic Activity. J.Biol.Chem. V. 272 18161 1997.
ISSN: ISSN 0021-9258
PubMed: 9218451
DOI: 10.1074/JBC.272.29.18161
Page generated: Fri Aug 28 12:34:12 2020
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