Zinc in PDB 1vsh: Asv Integrase Core Domain with Zn(II) Cofactors

The structure of Asv Integrase Core Domain with Zn(II) Cofactors, PDB code: 1vsh 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 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.080, 66.080, 80.960, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Asv Integrase Core Domain with Zn(II) Cofactors (pdb code 1vsh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Asv Integrase Core Domain with Zn(II) Cofactors, PDB code: 1vsh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Asv Integrase Core Domain with Zn(II) Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Asv Integrase Core Domain with Zn(II) Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn280 b:36.2 occ:1.00 O A:HOH284 2.0 36.6 1.0 OE2 A:GLU157 2.3 28.0 1.0 OD2 A:ASP64 2.3 18.1 1.0 O A:HOH282 2.4 22.8 1.0 OE1 A:GLU157 2.8 29.9 1.0 CD A:GLU157 2.9 30.5 1.0 CG A:ASP64 3.2 17.8 1.0 OD1 A:ASP64 3.5 12.8 1.0 ZN A:ZN281 3.6 28.4 1.0 ND2 A:ASN160 3.9 13.8 1.0 O A:PHE65 4.2 14.2 1.0 O A:HOH414 4.2 45.2 1.0 CG A:GLU157 4.4 26.1 1.0 O A:HOH307 4.4 32.2 1.0 CB A:ASP64 4.5 11.9 1.0 OD2 A:ASP121 4.6 19.9 1.0 O A:HOH398 4.9 50.0 1.0

Zinc binding site 2 out of 4 in the Asv Integrase Core Domain with Zn(II) Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Asv Integrase Core Domain with Zn(II) Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn281 b:28.4 occ:1.00 OD1 A:ASP64 2.1 12.8 1.0 O A:HOH283 2.1 36.3 1.0 OD2 A:ASP121 2.2 19.9 1.0 O A:HOH284 2.2 36.6 1.0 CG A:ASP121 3.1 20.2 1.0 CG A:ASP64 3.1 17.8 1.0 OD1 A:ASP121 3.3 16.9 1.0 ZN A:ZN280 3.6 36.2 1.0 OD2 A:ASP64 3.6 18.1 1.0 O A:HOH308 3.7 38.3 1.0 O A:HOH414 4.2 45.2 1.0 O A:PHE65 4.3 14.2 1.0 CB A:ASP121 4.4 21.6 1.0 CB A:ASP64 4.5 11.9 1.0 N A:PHE65 4.5 11.7 1.0 O A:HOH405 4.6 69.7 1.0 O A:HOH282 4.7 22.8 1.0 O A:HOH398 4.7 50.0 1.0 OE2 A:GLU157 4.8 28.0 1.0 CA A:ASP64 4.8 12.8 1.0 CE2 A:PHE126 4.9 17.8 1.0

Zinc binding site 3 out of 4 in the Asv Integrase Core Domain with Zn(II) Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Asv Integrase Core Domain with Zn(II) Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn285 b:50.6 occ:1.00 O A:HOH286 2.2 17.1 1.0 ND1 A:HIS103 2.2 20.8 1.0 O A:HOH288 2.4 20.6 1.0 O A:HOH287 2.7 44.9 1.0 CG A:HIS103 3.2 17.6 1.0 CE1 A:HIS103 3.2 22.2 1.0 CB A:HIS103 3.5 10.6 1.0 O A:HOH352 4.1 42.0 1.0 ND1 A:HIS93 4.1 15.7 1.0 O A:HOH392 4.2 53.4 1.0 O A:HOH409 4.3 56.6 1.0 NE2 A:HIS103 4.3 18.2 1.0 CD2 A:HIS103 4.3 16.8 1.0 CE1 A:HIS93 4.4 13.0 1.0 O A:HOH406 4.4 49.4 1.0 O A:HOH402 4.8 49.6 1.0 CA A:ALA100 4.9 10.9 1.0

Zinc binding site 4 out of 4 in the Asv Integrase Core Domain with Zn(II) Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Asv Integrase Core Domain with Zn(II) Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn289 b:50.7 occ:1.00 OH A:TYR194 2.1 21.0 1.0 ND1 A:HIS198 2.4 42.0 1.0 O A:HOH291 2.7 56.9 1.0 O A:HOH290 2.9 21.0 1.0 CZ A:TYR194 2.9 12.6 1.0 CE1 A:HIS198 3.3 41.5 1.0 CE1 A:TYR194 3.3 10.8 1.0 CG A:HIS198 3.4 41.3 1.0 CB A:HIS198 3.8 40.8 1.0 CE2 A:TYR194 3.9 11.3 1.0 CA A:HIS198 4.2 41.5 1.0 NE2 A:HIS198 4.4 37.4 1.0 CD2 A:HIS198 4.5 39.8 1.0 CD1 A:TYR194 4.6 11.2 1.0 C A:HIS198 4.9 45.8 1.0

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