Zinc in PDB 8w34: Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F

The structure of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F (pdb code 8w34). 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 Intasome Core Assembled with Wild-Type Integrase, 1F, PDB code: 8w34:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:76.6 occ:1.00 ND1 A:HIS16 2.1 42.3 1.0 NE2 A:HIS12 2.1 52.8 1.0 SG A:CYS40 2.3 50.0 1.0 SG A:CYS43 2.3 58.1 1.0 CE1 A:HIS12 2.8 46.5 1.0 CE1 A:HIS16 3.0 42.2 1.0 CB A:CYS40 3.1 42.6 1.0 CD2 A:HIS12 3.1 45.2 1.0 CG A:HIS16 3.2 38.5 1.0 CB A:CYS43 3.4 47.1 1.0 CB A:HIS16 3.6 41.4 1.0 ND1 A:HIS12 3.9 41.3 1.0 N A:CYS43 3.9 41.1 1.0 CA A:HIS16 4.0 41.6 1.0 CG A:HIS12 4.1 40.2 1.0 NE2 A:HIS16 4.1 40.2 1.0 CA A:CYS43 4.2 42.4 1.0 CD2 A:HIS16 4.2 35.2 1.0 C A:LYS42 4.5 42.2 1.0 CA A:CYS40 4.5 45.8 1.0 CB A:LYS42 4.6 40.3 1.0 O A:HIS12 4.7 48.0 1.0 NE2 I:GLN164 4.8 44.2 1.0 C A:HIS16 4.8 41.1 1.0 C A:CYS40 4.9 50.9 1.0 CA A:LYS42 4.9 42.1 1.0 O A:CYS40 4.9 49.6 1.0 N A:LYS42 5.0 43.9 1.0

Zinc binding site 2 out of 2 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:76.7 occ:1.00 ND1 I:HIS16 2.1 42.8 1.0 NE2 I:HIS12 2.1 53.0 1.0 SG I:CYS40 2.3 51.2 1.0 SG I:CYS43 2.3 58.6 1.0 CE1 I:HIS12 2.8 47.1 1.0 CE1 I:HIS16 3.0 42.5 1.0 CB I:CYS40 3.1 43.5 1.0 CD2 I:HIS12 3.1 45.7 1.0 CG I:HIS16 3.2 39.0 1.0 CB I:CYS43 3.4 46.7 1.0 CB I:HIS16 3.6 41.5 1.0 ND1 I:HIS12 3.9 42.4 1.0 N I:CYS43 4.0 40.9 1.0 CA I:HIS16 4.0 41.1 1.0 CG I:HIS12 4.0 40.3 1.0 NE2 I:HIS16 4.1 40.7 1.0 CA I:CYS43 4.2 42.3 1.0 CD2 I:HIS16 4.2 35.8 1.0 CA I:CYS40 4.5 47.3 1.0 C I:LYS42 4.5 42.5 1.0 CB I:LYS42 4.6 41.2 1.0 O I:HIS12 4.7 48.6 1.0 NE2 A:GLN164 4.8 43.7 1.0 C I:HIS16 4.8 41.1 1.0 O I:CYS40 4.9 50.8 1.0 C I:CYS40 4.9 51.9 1.0 CA I:LYS42 4.9 43.1 1.0 N I:LYS42 4.9 45.6 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