Zinc in PDB 8w09: Hiv-1 Wild-Type Intasome Core

The structure of Hiv-1 Wild-Type Intasome Core also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Fluorine	(F)	4 atoms

The binding sites of Zinc atom in the Hiv-1 Wild-Type Intasome Core (pdb code 8w09). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hiv-1 Wild-Type Intasome Core, PDB code: 8w09:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:69.7 occ:1.00 NE2 A:HIS12 2.0 36.6 1.0 ND1 A:HIS16 2.2 24.6 1.0 SG A:CYS40 2.2 43.6 1.0 SG A:CYS43 2.3 49.9 1.0 CD2 A:HIS12 2.7 30.3 1.0 CB A:CYS40 2.7 31.3 1.0 CE1 A:HIS12 2.9 35.5 1.0 CE1 A:HIS16 2.9 23.7 1.0 CG A:HIS16 3.3 15.7 1.0 CG A:HIS12 3.6 23.5 1.0 ND1 A:HIS12 3.7 30.7 1.0 CB A:HIS16 3.8 26.3 1.0 CB A:CYS43 3.9 35.5 1.0 CA A:HIS16 4.1 32.8 1.0 NE2 A:HIS16 4.1 19.5 1.0 CA A:CYS40 4.2 34.6 1.0 O A:HIS12 4.2 40.9 1.0 CD2 A:HIS16 4.3 14.9 1.0 N A:CYS43 4.4 31.8 1.0 C A:CYS40 4.7 40.9 1.0 CA A:CYS43 4.8 35.3 1.0 C A:HIS12 4.8 34.2 1.0 CB A:LYS42 4.9 28.1 1.0 CB A:HIS12 4.9 23.6 1.0

Zinc binding site 2 out of 2 in the Hiv-1 Wild-Type Intasome Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hiv-1 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn303 b:61.9 occ:1.00 NE2 I:HIS12 2.1 35.3 1.0 ND1 I:HIS16 2.2 22.0 1.0 SG I:CYS40 2.3 39.0 1.0 SG I:CYS43 2.3 51.6 1.0 CB I:CYS40 2.8 27.2 1.0 CD2 I:HIS12 2.8 31.0 1.0 CE1 I:HIS12 2.9 33.8 1.0 CE1 I:HIS16 2.9 23.7 1.0 CG I:HIS16 3.3 13.2 1.0 CB I:CYS43 3.5 32.5 1.0 ND1 I:HIS12 3.8 26.9 1.0 CG I:HIS12 3.8 24.8 1.0 CB I:HIS16 3.8 26.1 1.0 N I:CYS43 4.1 30.2 1.0 NE2 I:HIS16 4.1 20.6 1.0 CA I:HIS16 4.2 31.9 1.0 CA I:CYS40 4.3 32.2 1.0 CD2 I:HIS16 4.3 13.4 1.0 O I:HIS12 4.4 39.7 1.0 CA I:CYS43 4.4 31.6 1.0 C I:LYS42 4.7 31.2 1.0 C I:CYS40 4.7 37.3 1.0 CB I:LYS42 4.9 30.0 1.0 N I:LYS42 5.0 33.2 1.0 O I:VAL37 5.0 27.0 1.0 O I:CYS40 5.0 39.2 1.0

M.Li, R.Yang, X.Chen, H.Wang, R.Ghirlando, E.K.Dimitriadis, R.Craigie. Hiv-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active For Concerted Dna Integration in Vitro. J.Mol.Biol. 68557 2024.
ISSN: ESSN 1089-8638
PubMed: 38582148
DOI: 10.1016/J.JMB.2024.168557