Zinc in PDB 9c9m: Hiv-1 Intasome Core Bound with Dtg

The structure of Hiv-1 Intasome Core Bound with Dtg 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 Bound with Dtg (pdb code 9c9m). 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 Bound with Dtg, PDB code: 9c9m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:27.1 occ:1.00 ND1 A:HIS16 2.1 9.3 1.0 NE2 A:HIS12 2.1 18.2 1.0 SG A:CYS40 2.2 17.5 1.0 SG A:CYS43 2.2 19.4 1.0 CE1 A:HIS12 2.8 14.4 1.0 CE1 A:HIS16 3.0 10.9 1.0 CD2 A:HIS12 3.1 12.2 1.0 CG A:HIS16 3.1 10.4 1.0 CB A:CYS40 3.2 14.4 1.0 CB A:HIS16 3.5 9.6 1.0 CB A:CYS43 3.5 12.2 1.0 ND1 A:HIS12 3.9 15.5 1.0 CA A:HIS16 4.0 10.5 1.0 N A:CYS43 4.0 12.7 1.0 CG A:HIS12 4.0 17.1 1.0 NE2 A:HIS16 4.2 12.9 1.0 CD2 A:HIS16 4.2 10.1 1.0 CA A:CYS43 4.3 15.3 1.0 CB A:LYS42 4.5 17.3 1.0 C A:LYS42 4.5 10.9 1.0 CA A:CYS40 4.6 16.0 1.0 O A:HIS12 4.7 14.6 1.0 NE2 I:GLN164 4.7 10.4 1.0 C A:HIS16 4.9 10.2 1.0 CA A:LYS42 4.9 12.6 1.0 C A:CYS40 5.0 19.6 1.0 N A:LYS42 5.0 16.0 1.0 O A:CYS40 5.0 21.5 1.0

Zinc binding site 2 out of 2 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn303 b:28.1 occ:1.00 ND1 I:HIS16 2.1 8.8 1.0 NE2 I:HIS12 2.1 17.8 1.0 SG I:CYS40 2.2 17.4 1.0 SG I:CYS43 2.2 19.6 1.0 CE1 I:HIS12 2.8 14.7 1.0 CE1 I:HIS16 3.0 10.6 1.0 CD2 I:HIS12 3.1 12.9 1.0 CG I:HIS16 3.1 10.1 1.0 CB I:CYS40 3.2 14.4 1.0 CB I:HIS16 3.5 9.7 1.0 CB I:CYS43 3.5 11.6 1.0 ND1 I:HIS12 3.9 15.3 1.0 CA I:HIS16 4.0 10.9 1.0 N I:CYS43 4.0 13.2 1.0 CG I:HIS12 4.0 18.1 1.0 NE2 I:HIS16 4.2 11.9 1.0 CD2 I:HIS16 4.2 9.8 1.0 CA I:CYS43 4.3 15.8 1.0 CB I:LYS42 4.5 19.1 1.0 C I:LYS42 4.5 11.0 1.0 CA I:CYS40 4.6 15.8 1.0 O I:HIS12 4.7 14.8 1.0 NE2 A:GLN164 4.7 9.8 1.0 C I:HIS16 4.9 10.5 1.0 CA I:LYS42 4.9 13.2 1.0 N I:LYS42 5.0 16.6 1.0 C I:CYS40 5.0 19.6 1.0 O I:CYS40 5.0 21.5 1.0

M.Li, X.Chen, Z.Li, Y.Cui, A.Engelman, R.Craigie. Hiv-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies By Cryo-Em and Reveal the Role of the Integrase C-Terminal Tail in Hiv-1 Integration Viruses 2024.
ISSN: ESSN 1999-4915