Zinc in PDB 3hpg: Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces

The structure of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces, PDB code: 3hpg was solved by S.Hare, A.Labeja, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.67 / 3.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.104, 148.904, 91.076, 90.00, 113.41, 90.00
R / Rfree (%)	21.2 / 25.3

The binding sites of Zinc atom in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces (pdb code 3hpg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces, PDB code: 3hpg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn220 b:98.7 occ:1.00 ND1 A:HIS16 2.2 0.3 1.0 NE2 A:HIS12 2.4 93.8 1.0 SG A:CYS40 2.4 0.9 1.0 SG A:CYS43 2.5 96.5 1.0 CE1 A:HIS16 2.9 0.2 1.0 CB A:CYS43 3.1 0.3 1.0 CB A:CYS40 3.2 0.1 1.0 CG A:HIS16 3.3 0.3 1.0 CE1 A:HIS12 3.3 92.2 1.0 CD2 A:HIS12 3.3 97.2 1.0 N A:CYS43 3.6 98.8 1.0 CB A:HIS16 3.8 99.7 1.0 CA A:CYS43 3.8 96.8 1.0 NE2 A:HIS16 4.1 0.1 1.0 CD2 A:HIS16 4.2 99.1 1.0 CA A:HIS16 4.3 0.0 1.0 CB A:VAL42 4.3 85.4 1.0 ND1 A:HIS12 4.4 94.5 1.0 CG A:HIS12 4.4 97.8 1.0 CA A:CYS40 4.6 0.4 1.0 C A:VAL42 4.6 84.6 1.0 O A:CYS40 4.8 0.8 1.0 C A:CYS40 4.9 0.5 1.0 CA A:VAL42 4.9 87.3 1.0 CG1 A:VAL42 5.0 77.9 1.0

Zinc binding site 2 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn220 b:78.3 occ:1.00 ND1 B:HIS16 2.1 76.7 1.0 NE2 B:HIS12 2.2 86.8 1.0 SG B:CYS40 2.4 89.3 1.0 SG B:CYS43 2.5 81.6 1.0 CE1 B:HIS16 3.0 76.7 1.0 CB B:CYS43 3.1 87.2 1.0 CG B:HIS16 3.1 73.3 1.0 CE1 B:HIS12 3.1 85.7 1.0 CD2 B:HIS12 3.2 84.9 1.0 CB B:CYS40 3.3 94.2 1.0 CB B:HIS16 3.6 72.5 1.0 N B:CYS43 3.7 86.7 1.0 CA B:CYS43 3.9 84.9 1.0 NE2 B:HIS16 4.1 73.3 1.0 CA B:HIS16 4.1 71.2 1.0 CD2 B:HIS16 4.2 71.2 1.0 ND1 B:HIS12 4.2 83.1 1.0 CG B:HIS12 4.3 82.5 1.0 CB B:VAL42 4.5 83.8 1.0 CA B:CYS40 4.7 98.7 1.0 C B:VAL42 4.7 87.8 1.0 C B:HIS16 4.8 71.1 1.0 O B:CYS40 5.0 98.0 1.0 O B:HIS12 5.0 75.2 1.0

Zinc binding site 3 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn220 b:77.2 occ:1.00 NE2 C:HIS12 2.2 85.5 1.0 ND1 C:HIS16 2.2 86.3 1.0 SG C:CYS40 2.3 87.4 1.0 SG C:CYS43 2.6 82.1 1.0 CE1 C:HIS16 3.0 87.5 1.0 CB C:CYS40 3.0 88.0 1.0 CE1 C:HIS12 3.1 84.3 1.0 CB C:CYS43 3.1 83.2 1.0 CD2 C:HIS12 3.1 86.5 1.0 CG C:HIS16 3.3 85.0 1.0 N C:CYS43 3.7 84.2 1.0 CB C:HIS16 3.8 83.4 1.0 CA C:CYS43 4.0 82.8 1.0 NE2 C:HIS16 4.1 87.0 1.0 ND1 C:HIS12 4.2 84.5 1.0 CG C:HIS12 4.2 85.9 1.0 CA C:HIS16 4.3 83.5 1.0 CD2 C:HIS16 4.3 85.4 1.0 CA C:CYS40 4.5 89.4 1.0 CB C:VAL42 4.5 78.5 1.0 C C:VAL42 4.8 77.0 1.0 O C:CYS40 4.8 87.3 1.0 C C:CYS40 4.8 88.7 1.0

Zinc binding site 4 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn220 b:72.4 occ:1.00 SG D:CYS40 2.2 79.0 1.0 ND1 D:HIS16 2.3 89.2 1.0 NE2 D:HIS12 2.3 70.4 1.0 SG D:CYS43 2.3 77.5 1.0 CB D:CYS43 2.9 78.1 1.0 CE1 D:HIS16 3.0 90.3 1.0 CB D:CYS40 3.2 78.5 1.0 CE1 D:HIS12 3.2 69.4 1.0 CG D:HIS16 3.3 88.6 1.0 CD2 D:HIS12 3.3 71.1 1.0 N D:CYS43 3.6 79.9 1.0 CB D:HIS16 3.7 87.5 1.0 CA D:CYS43 3.8 78.7 1.0 NE2 D:HIS16 4.2 89.2 1.0 CA D:HIS16 4.2 86.9 1.0 CD2 D:HIS16 4.3 88.1 1.0 ND1 D:HIS12 4.3 69.3 1.0 CG D:HIS12 4.4 70.4 1.0 CB D:VAL42 4.4 78.2 1.0 CA D:CYS40 4.6 79.3 1.0 C D:VAL42 4.6 76.7 1.0 O D:CYS40 4.8 78.6 1.0 C D:CYS40 4.9 79.4 1.0 C D:HIS16 5.0 85.6 1.0

Zinc binding site 5 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn220 b:88.8 occ:1.00 ND1 E:HIS16 2.2 0.6 1.0 NE2 E:HIS12 2.2 88.2 1.0 SG E:CYS40 2.4 85.5 1.0 SG E:CYS43 2.6 0.3 1.0 CE1 E:HIS16 3.0 0.9 1.0 CE1 E:HIS12 3.1 87.8 1.0 CB E:CYS43 3.1 0.6 1.0 CD2 E:HIS12 3.2 88.2 1.0 CB E:CYS40 3.2 87.1 1.0 CG E:HIS16 3.2 0.4 1.0 CB E:HIS16 3.7 0.9 1.0 N E:CYS43 3.7 0.5 1.0 CA E:CYS43 3.9 0.3 1.0 NE2 E:HIS16 4.1 0.1 1.0 CA E:HIS16 4.1 1.0 1.0 ND1 E:HIS12 4.2 87.7 1.0 CD2 E:HIS16 4.3 0.1 1.0 CG E:HIS12 4.3 87.9 1.0 CB E:VAL42 4.5 0.8 1.0 CA E:CYS40 4.7 88.5 1.0 C E:VAL42 4.7 0.2 1.0 C E:HIS16 4.9 0.8 1.0 O E:CYS40 4.9 87.8 1.0

Zinc binding site 6 out of 6 in the Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Visna Virus Integrase (Residues 1-219) in Complex with Ledgf Ibd: Examples of Open Integrase Dimer-Dimer Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn220 b:73.2 occ:1.00 ND1 F:HIS16 2.2 74.3 1.0 NE2 F:HIS12 2.4 79.7 1.0 SG F:CYS43 2.4 88.0 1.0 SG F:CYS40 2.5 91.2 1.0 CB F:CYS43 3.0 89.6 1.0 CE1 F:HIS16 3.0 75.3 1.0 CE1 F:HIS12 3.2 78.6 1.0 CB F:CYS40 3.2 93.3 1.0 CG F:HIS16 3.2 71.7 1.0 CD2 F:HIS12 3.4 81.7 1.0 N F:CYS43 3.6 89.7 1.0 CB F:HIS16 3.7 69.9 1.0 CA F:CYS43 3.8 88.0 1.0 NE2 F:HIS16 4.1 73.5 1.0 CA F:HIS16 4.2 71.5 1.0 CD2 F:HIS16 4.3 71.2 1.0 ND1 F:HIS12 4.3 79.8 1.0 CG F:HIS12 4.4 81.8 1.0 CB F:VAL42 4.4 83.8 1.0 C F:VAL42 4.6 81.9 1.0 CA F:CYS40 4.6 95.3 1.0 O F:CYS40 4.8 90.8 1.0 C F:CYS40 4.9 93.1 1.0 C F:HIS16 5.0 69.9 1.0 CA F:VAL42 5.0 83.8 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