Magnesium in PDB 8cbv: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916, PDB code: 8cbv was solved by M.R.Singer, V.E.Pye, Z.Yu, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.11 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.275, 65.083, 70.588, 90, 101.64, 90
R / Rfree (%)	18.7 / 23

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 (pdb code 8cbv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916, PDB code: 8cbv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:35.5 occ:1.00 O B:HOH616 2.0 37.7 1.0 O B:HOH611 2.1 40.1 1.0 O B:HOH663 2.1 35.9 1.0 O B:HOH648 2.1 35.8 1.0 OD2 B:ASP116 2.2 41.2 1.0 OD1 B:ASP64 2.2 34.6 1.0 CG B:ASP64 3.2 41.2 1.0 CG B:ASP116 3.2 41.4 1.0 OD2 B:ASP64 3.4 39.7 1.0 OD1 B:ASP116 3.6 41.6 1.0 O B:HOH622 4.1 33.4 1.0 O B:HOH677 4.1 65.6 1.0 O B:HOH626 4.2 34.4 1.0 O B:CYS65 4.3 32.2 1.0 N B:CYS65 4.5 32.7 1.0 O B:HOH610 4.5 38.2 1.0 CB B:ASP64 4.6 32.5 1.0 CB B:ASP116 4.6 37.4 1.0 CA B:ASP64 4.9 32.0 1.0 CE2 B:PHE121 5.0 32.0 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148916 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg506 b:45.4 occ:1.00 O D:HOH619 1.9 47.0 1.0 O D:HOH623 2.0 41.8 1.0 OD2 D:ASP116 2.1 51.3 1.0 OD1 D:ASP64 2.1 41.4 1.0 O D:HOH640 2.1 44.4 1.0 O D:HOH664 2.2 45.5 1.0 CG D:ASP64 3.1 45.7 1.0 CG D:ASP116 3.2 45.1 1.0 OD2 D:ASP64 3.3 50.6 1.0 OD1 D:ASP116 3.6 45.5 1.0 O D:HOH642 3.9 65.9 1.0 O D:HOH604 4.1 44.6 1.0 O D:CYS65 4.2 38.2 1.0 O D:HOH608 4.4 48.8 1.0 N D:CYS65 4.4 37.6 1.0 CB D:ASP64 4.4 41.1 1.0 CB D:ASP116 4.5 51.6 1.0 O D:HOH603 4.6 53.4 1.0 CA D:ASP64 4.8 37.9 1.0

D.Bonnard, E.Le Rouzic, M.R.Singer, Z.Yu, F.Le Strat, C.Batisse, J.Batisse, C.Amadori, S.Chasset, V.E.Pye, S.Emiliani, B.Ledoussal, M.Ruff, F.Moreau, P.Cherepanov, R.Benarousa. Biological and Structural Analyses of New Potent Allosteric Inhibitors of Hiv-1 Integrase Antimicrob.Agents Chemother. 2023.
ISSN: ESSN 1098-6596