Zinc in PDB 3o4n: Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0

The structure of Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0, PDB code: 3o4n was solved by A.Ballandras, X.Robert, P.Gouet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	107.500, 107.500, 50.920, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22.6

The binding sites of Zinc atom in the Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0 (pdb code 3o4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0, PDB code: 3o4n:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:29.6 occ:1.00 O A:HOH359 2.0 25.9 1.0 OD1 A:ASP64 2.1 22.5 1.0 O A:HOH358 2.1 31.5 1.0 OD2 A:ASP121 2.2 26.1 1.0 CG A:ASP64 2.7 20.7 1.0 OD2 A:ASP64 2.7 26.9 1.0 CG A:ASP121 3.2 24.7 1.0 OD1 A:ASP121 3.5 24.3 1.0 O A:HOH200 4.1 26.6 1.0 CB A:ASP64 4.2 20.3 1.0 O A:HOH331 4.3 40.7 1.0 O A:PHE65 4.3 22.3 1.0 N A:PHE65 4.4 19.7 1.0 CB A:ASP121 4.6 26.7 1.0 CA A:ASP64 4.7 20.7 1.0 CE2 A:PHE126 4.8 23.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:26.9 occ:1.00 ND1 B:HIS103 2.0 19.6 1.0 ND1 A:HIS103 2.0 19.4 1.0 O A:HOH271 2.2 9.9 1.0 O A:HOH257 2.3 10.5 1.0 CE1 B:HIS103 3.0 19.9 1.0 CG A:HIS103 3.0 20.3 1.0 CE1 A:HIS103 3.1 20.8 1.0 CG B:HIS103 3.1 19.1 1.0 CB A:HIS103 3.4 20.8 1.0 CB B:HIS103 3.5 19.1 1.0 NE2 B:HIS103 4.1 19.0 1.0 CD2 B:HIS103 4.2 22.1 1.0 NE2 A:HIS103 4.2 22.7 1.0 CD2 A:HIS103 4.2 24.9 1.0 O A:HOH317 4.2 31.7 1.0 O A:HOH338 4.2 36.3 1.0 CG1 A:VAL99 4.9 25.6 1.0 CA A:HIS103 4.9 18.8 1.0 CG1 B:VAL99 4.9 23.9 1.0 NH2 A:ARG95 5.0 46.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Rous Associated Virus Integrase Catalytic Domain in Mes Buffer pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:35.5 occ:1.00 OD2 B:ASP121 2.0 28.6 1.0 OD1 B:ASP64 2.1 26.4 1.0 O B:HOH313 2.1 25.9 1.0 O B:HOH268 2.2 33.8 1.0 CG B:ASP64 2.9 28.6 1.0 OD2 B:ASP64 3.0 30.2 1.0 CG B:ASP121 3.2 28.1 1.0 OD1 B:ASP121 3.5 32.1 1.0 O B:HOH205 3.9 25.6 1.0 O B:HOH382 4.0 40.8 1.0 O B:HOH220 4.2 47.0 1.0 O B:PHE65 4.2 30.1 1.0 CB B:ASP64 4.3 25.2 1.0 N B:PHE65 4.4 24.6 1.0 CB B:ASP121 4.5 31.4 1.0 CE2 B:PHE126 4.7 27.9 1.0 CA B:ASP64 4.7 25.6 1.0

A.Ballandras, K.Moreau, X.Robert, M.P.Confort, R.Merceron, R.Haser, C.Ronfort, P.Gouet. A Crystal Structure of the Catalytic Core Domain of An Avian Sarcoma and Leukemia Virus Integrase Suggests An Alternate Dimeric Assembly. Plos One V. 6 23032 2011.
ISSN: ESSN 1932-6203
PubMed: 21857987
DOI: 10.1371/JOURNAL.PONE.0023032