Zinc in PDB 3hph: Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd

The structure of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd, PDB code: 3hph was solved by S.Hare, J.Wang, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.01 / 2.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.870, 83.150, 115.300, 90.00, 101.96, 90.00
R / Rfree (%)	22.6 / 25.3

The binding sites of Zinc atom in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd (pdb code 3hph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd, PDB code: 3hph:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn220 b:30.6 occ:1.00 NE2 A:HIS12 2.1 23.1 1.0 ND1 A:HIS16 2.2 24.1 1.0 SG A:CYS40 2.4 37.4 1.0 SG A:CYS43 2.4 38.0 1.0 CE1 A:HIS12 3.0 23.9 1.0 CD2 A:HIS12 3.1 23.8 1.0 CG A:HIS16 3.1 24.4 1.0 CE1 A:HIS16 3.3 24.8 1.0 CB A:HIS16 3.3 23.5 1.0 CB A:CYS40 3.6 38.4 1.0 CB A:CYS43 3.7 37.6 1.0 ND1 A:HIS12 4.0 24.5 1.0 CA A:HIS16 4.0 23.5 1.0 CG A:HIS12 4.1 25.4 1.0 N A:CYS43 4.1 37.8 1.0 CD2 A:HIS16 4.3 24.6 1.0 NE2 A:HIS16 4.3 24.9 1.0 CA A:CYS43 4.4 37.7 1.0 O A:HIS12 4.4 26.0 1.0 CB A:VAL42 4.5 38.4 1.0 C A:VAL42 4.7 38.1 1.0 C A:HIS16 4.9 23.8 1.0 CA A:CYS40 4.9 38.4 1.0 CA A:VAL42 5.0 38.5 1.0

Zinc binding site 2 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn220 b:19.0 occ:1.00 NE2 B:HIS12 2.0 17.2 1.0 ND1 B:HIS16 2.1 18.2 1.0 SG B:CYS43 2.2 38.4 1.0 SG B:CYS40 2.4 36.8 1.0 CE1 B:HIS12 2.8 19.5 1.0 CE1 B:HIS16 3.0 17.8 1.0 CD2 B:HIS12 3.1 19.8 1.0 CG B:HIS16 3.2 18.7 1.0 CB B:CYS40 3.3 39.1 1.0 CB B:CYS43 3.5 39.5 1.0 CB B:HIS16 3.6 17.1 1.0 ND1 B:HIS12 3.9 20.7 1.0 N B:CYS43 3.9 39.7 1.0 CG B:HIS12 4.0 21.0 1.0 CA B:HIS16 4.1 17.7 1.0 NE2 B:HIS16 4.2 17.9 1.0 CA B:CYS43 4.3 39.7 1.0 CD2 B:HIS16 4.3 18.5 1.0 O B:HIS12 4.4 23.1 1.0 CB B:VAL42 4.6 40.7 1.0 CA B:CYS40 4.8 39.3 1.0 O B:HOH242 4.8 16.7 1.0 C B:VAL42 4.8 40.2 1.0 C B:HIS16 4.9 17.5 1.0

Zinc binding site 3 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn220 b:20.7 occ:1.00 NE2 C:HIS12 2.0 17.0 1.0 ND1 C:HIS16 2.1 18.1 1.0 SG C:CYS43 2.1 37.8 1.0 SG C:CYS40 2.4 37.0 1.0 CE1 C:HIS12 2.7 19.6 1.0 CE1 C:HIS16 3.0 17.7 1.0 CD2 C:HIS12 3.1 19.9 1.0 CG C:HIS16 3.2 18.6 1.0 CB C:CYS40 3.4 39.2 1.0 CB C:CYS43 3.4 39.5 1.0 CB C:HIS16 3.5 17.2 1.0 ND1 C:HIS12 3.8 21.0 1.0 N C:CYS43 3.9 39.7 1.0 CG C:HIS12 4.0 21.2 1.0 CA C:HIS16 4.0 17.8 1.0 NE2 C:HIS16 4.2 17.8 1.0 CD2 C:HIS16 4.2 18.7 1.0 CA C:CYS43 4.3 39.6 1.0 O C:HIS12 4.5 23.2 1.0 CB C:VAL42 4.6 40.7 1.0 CA C:CYS40 4.8 39.3 1.0 C C:VAL42 4.8 40.2 1.0 C C:HIS16 4.9 17.6 1.0 O C:HOH244 5.0 8.2 1.0 O C:HIS16 5.0 18.0 1.0

Zinc binding site 4 out of 4 in the Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Closed Tetramer of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn220 b:34.4 occ:1.00 NE2 D:HIS12 2.2 23.2 1.0 ND1 D:HIS16 2.2 24.2 1.0 SG D:CYS40 2.3 37.5 1.0 SG D:CYS43 2.5 38.2 1.0 CD2 D:HIS12 3.0 23.9 1.0 CE1 D:HIS12 3.1 23.8 1.0 CG D:HIS16 3.1 24.4 1.0 CE1 D:HIS16 3.2 24.9 1.0 CB D:HIS16 3.4 23.6 1.0 CB D:CYS40 3.5 38.5 1.0 CB D:CYS43 3.7 37.7 1.0 N D:CYS43 4.1 37.8 1.0 ND1 D:HIS12 4.1 24.4 1.0 CG D:HIS12 4.1 25.5 1.0 CA D:HIS16 4.1 23.6 1.0 CD2 D:HIS16 4.3 24.6 1.0 NE2 D:HIS16 4.3 24.9 1.0 CA D:CYS43 4.4 37.7 1.0 O D:HIS12 4.4 26.1 1.0 CB D:VAL42 4.5 38.5 1.0 C D:VAL42 4.7 38.1 1.0 CA D:CYS40 4.9 38.4 1.0 CA D:VAL42 4.9 38.5 1.0 N D:VAL42 5.0 39.1 1.0

S.Hare, F.Di Nunzio, A.Labeja, J.Wang, A.Engelman, P.Cherepanov. Structural Basis For Functional Tetramerization of Lentiviral Integrase Plos Pathog. V. 5 E1000 2009.
ISSN: ISSN 1553-7366
PubMed: 19609359
DOI: 10.1371/JOURNAL.PPAT.1000515