Zinc in PDB 8w2r: Hiv-1 P5-in Intasome Core

The structure of Hiv-1 P5-in 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 P5-in Intasome Core (pdb code 8w2r). 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 P5-in Intasome Core, PDB code: 8w2r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:116.2 occ:1.00 ND1 A:HIS16 2.1 57.0 1.0 NE2 A:HIS12 2.1 67.2 1.0 SG A:CYS40 2.2 73.8 1.0 SG A:CYS43 2.3 61.8 1.0 CE1 A:HIS12 2.4 64.7 1.0 CB A:CYS40 2.9 61.2 1.0 CE1 A:HIS16 3.1 52.3 1.0 CG A:HIS16 3.1 50.4 1.0 CD2 A:HIS12 3.1 57.5 1.0 CB A:HIS16 3.4 51.0 1.0 ND1 A:HIS12 3.5 64.3 1.0 CA A:HIS16 3.6 52.1 1.0 CB A:CYS43 3.6 62.8 1.0 CG A:HIS12 3.8 50.4 1.0 NE2 A:HIS16 4.2 52.6 1.0 CD2 A:HIS16 4.2 47.1 1.0 CA A:CYS40 4.4 66.0 1.0 C A:HIS16 4.4 45.4 1.0 O A:HIS12 4.5 66.4 1.0 N A:CYS43 4.5 58.0 1.0 CA A:CYS43 4.6 53.6 1.0 N A:HIS16 4.6 64.0 1.0 O A:HIS16 4.9 49.5 1.0 O A:CYS40 4.9 60.9 1.0 C A:CYS40 4.9 65.5 1.0

Zinc binding site 2 out of 2 in the Hiv-1 P5-in 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 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn303 b:120.5 occ:1.00 ND1 I:HIS16 2.1 53.8 1.0 NE2 I:HIS12 2.1 63.6 1.0 SG I:CYS43 2.2 58.9 1.0 SG I:CYS40 2.2 71.2 1.0 CE1 I:HIS12 2.5 61.3 1.0 CB I:CYS40 2.8 61.1 1.0 CE1 I:HIS16 3.0 48.7 1.0 CD2 I:HIS12 3.0 57.9 1.0 CG I:HIS16 3.1 46.6 1.0 ND1 I:HIS12 3.5 61.0 1.0 CB I:HIS16 3.5 46.1 1.0 CA I:HIS16 3.6 48.2 1.0 CG I:HIS12 3.8 49.7 1.0 CB I:CYS43 3.8 62.0 1.0 NE2 I:HIS16 4.1 47.3 1.0 O I:HIS12 4.2 65.6 1.0 CD2 I:HIS16 4.2 43.3 1.0 CA I:CYS40 4.3 65.1 1.0 C I:HIS16 4.5 43.2 1.0 N I:CYS43 4.6 56.7 1.0 N I:HIS16 4.7 60.9 1.0 CA I:CYS43 4.7 53.5 1.0 C I:CYS40 4.9 63.4 1.0 O I:HIS16 5.0 47.5 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