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Magnesium in PDB 8cbs: Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148871

Protein crystallography data

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148871, PDB code: 8cbs 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) 52.16 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.228, 64.853, 70.439, 90, 101.5, 90
R / Rfree (%) 16.7 / 19.8

Other elements in 8cbs:

The structure of Hiv-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor Mut-148871 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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-148871 (pdb code 8cbs). 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-148871, PDB code: 8cbs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8cbs

Go back to Magnesium Binding Sites List in 8cbs
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-148871


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-148871 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:36.9
occ:1.00
O B:HOH731 2.0 36.1 1.0
O B:HOH728 2.1 37.0 1.0
O B:HOH721 2.1 39.5 1.0
OD1 B:ASP64 2.2 37.3 1.0
OD2 B:ASP116 2.2 39.9 1.0
CG B:ASP64 3.1 40.2 1.0
CG B:ASP116 3.2 44.0 1.0
OD2 B:ASP64 3.4 41.5 1.0
OD1 B:ASP116 3.5 40.8 1.0
O B:HOH719 3.8 65.7 1.0
O B:HOH729 4.1 37.5 1.0
O B:HOH712 4.2 39.2 1.0
O B:CYS65 4.3 37.1 1.0
N B:CYS65 4.4 32.9 1.0
O B:HOH713 4.5 40.8 1.0
CB B:ASP64 4.5 34.5 1.0
CB B:ASP116 4.6 45.3 1.0
CA B:ASP64 4.9 33.7 1.0
O B:HOH792 4.9 74.8 1.0

Magnesium binding site 2 out of 2 in 8cbs

Go back to Magnesium Binding Sites List in 8cbs
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-148871


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-148871 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg307

b:44.7
occ:1.00
O D:HOH437 2.0 48.6 1.0
O D:HOH470 2.1 49.2 1.0
O D:HOH430 2.1 44.1 1.0
OD2 D:ASP116 2.1 48.4 1.0
O D:HOH431 2.2 45.4 1.0
OD1 D:ASP64 2.2 42.2 1.0
CG D:ASP64 3.2 41.3 1.0
CG D:ASP116 3.2 52.2 1.0
OD2 D:ASP64 3.5 46.8 1.0
OD1 D:ASP116 3.6 45.8 1.0
O D:HOH415 4.0 44.1 1.0
O D:HOH419 4.3 56.2 1.0
O D:CYS65 4.3 41.5 1.0
N D:CYS65 4.4 35.3 1.0
O D:HOH407 4.4 51.0 1.0
CB D:ASP116 4.5 50.4 1.0
CB D:ASP64 4.6 39.4 1.0
CA D:ASP64 4.9 37.4 1.0
C2 D:EDO306 4.9 59.1 1.0
CE2 D:PHE121 5.0 42.3 1.0

Reference:

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
Page generated: Thu Oct 3 20:32:17 2024

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