Magnesium in PDB 8fnm: Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound

The structure of Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Magnesium atom in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound (pdb code 8fnm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound, PDB code: 8fnm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:47.5 occ:1.00 O A:HOH416 2.0 34.6 1.0 OD2 A:ASP116 2.1 44.1 1.0 OD1 A:ASP64 2.1 40.6 1.0 OAC A:DLU304 2.1 42.2 1.0 OAE A:DLU304 2.1 45.1 1.0 O A:HOH410 2.2 42.6 1.0 CG A:ASP116 3.0 37.3 1.0 CG A:ASP64 3.1 39.9 1.0 CAS A:DLU304 3.1 35.7 1.0 CAW A:DLU304 3.3 31.0 1.0 OD2 A:ASP64 3.4 39.6 1.0 OD1 A:ASP116 3.5 49.0 1.0 NZ A:LYS148 3.6 33.1 1.0 CAY A:DLU304 3.7 28.1 1.0 MG A:MG302 3.9 34.3 1.0 CB A:ASP116 4.0 29.1 1.0 NBC A:DLU304 4.1 31.8 1.0 CB A:ASP64 4.4 37.2 1.0 O A:HOH420 4.4 40.1 1.0 CBA A:DLU304 4.4 36.4 1.0 CAZ A:DLU304 4.5 33.9 1.0 N A:CYS65 4.5 45.0 1.0 OE2 A:GLU152 4.6 38.6 1.0 O A:CYS65 4.6 46.7 1.0 OAD A:DLU304 4.7 45.1 1.0 N1 F:DA21 4.7 16.1 0.5 CA A:ASP64 4.7 31.4 1.0 CAM A:DLU304 4.8 39.2 1.0 CE A:LYS148 4.9 39.3 1.0 C2 F:DA21 4.9 14.9 0.5

Magnesium binding site 2 out of 4 in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.3 occ:1.00 OAD A:DLU304 1.8 45.1 1.0 OE2 A:GLU152 2.1 38.6 1.0 OD2 A:ASP64 2.1 39.6 1.0 O A:HOH420 2.1 40.1 1.0 OE1 A:GLU152 2.1 37.5 1.0 OAE A:DLU304 2.3 45.1 1.0 CD A:GLU152 2.4 37.0 1.0 CAZ A:DLU304 2.6 33.9 1.0 CAW A:DLU304 2.8 31.0 1.0 CG A:ASP64 3.2 39.9 1.0 OD1 A:ASP64 3.7 40.6 1.0 NZ A:LYS148 3.8 33.1 1.0 CG A:GLU152 3.9 26.6 1.0 MG A:MG301 3.9 47.5 1.0 CAX A:DLU304 4.0 27.5 1.0 ND2 A:ASN155 4.1 36.5 1.0 O A:HOH410 4.2 42.6 1.0 C5' F:DA21 4.3 18.4 0.5 CAY A:DLU304 4.3 28.1 1.0 CB A:ASP64 4.4 37.2 1.0 FAG A:DLU304 4.5 41.5 1.0 NAP A:DLU304 4.5 30.7 1.0 C2 F:DA21 4.6 14.9 0.5 CAR A:DLU304 4.7 32.4 1.0 OAC A:DLU304 4.7 42.2 1.0 CB A:GLU152 4.7 30.9 1.0 O A:CYS65 4.8 46.7 1.0 OP1 F:DA21 4.8 16.9 0.5 OP1 F:DA21 4.8 17.2 0.5 O3' F:DC20 4.9 15.3 1.0 N3 F:DA21 4.9 13.3 0.5 CA A:GLU152 5.0 23.2 1.0

Magnesium binding site 3 out of 4 in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:47.5 occ:1.00 O G:HOH416 2.0 34.6 1.0 OD2 G:ASP116 2.1 44.1 1.0 OD1 G:ASP64 2.1 40.6 1.0 OAE G:DLU304 2.1 45.1 1.0 OAC G:DLU304 2.1 42.2 1.0 O G:HOH410 2.2 42.6 1.0 CG G:ASP116 3.0 37.3 1.0 CG G:ASP64 3.1 39.9 1.0 CAS G:DLU304 3.1 35.7 1.0 CAW G:DLU304 3.2 31.0 1.0 OD2 G:ASP64 3.4 39.6 1.0 OD1 G:ASP116 3.5 49.0 1.0 NZ G:LYS148 3.6 33.1 1.0 CAY G:DLU304 3.7 28.1 1.0 MG G:MG302 3.9 34.3 1.0 CB G:ASP116 4.0 29.1 1.0 NBC G:DLU304 4.1 31.8 1.0 CB G:ASP64 4.4 37.2 1.0 O G:HOH420 4.4 40.1 1.0 CBA G:DLU304 4.4 36.4 1.0 CAZ G:DLU304 4.5 33.9 1.0 N G:CYS65 4.5 45.0 1.0 OE2 G:GLU152 4.6 38.6 1.0 O G:CYS65 4.6 46.7 1.0 OAD G:DLU304 4.7 45.1 1.0 N1 L:DA21 4.7 16.1 0.5 CA G:ASP64 4.7 31.4 1.0 CAM G:DLU304 4.8 39.2 1.0 CE G:LYS148 4.9 39.3 1.0 C2 L:DA21 4.9 14.9 0.5

Magnesium binding site 4 out of 4 in the Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of G140A/Q148K Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:34.3 occ:1.00 OAD G:DLU304 1.8 45.1 1.0 OE2 G:GLU152 2.1 38.6 1.0 OD2 G:ASP64 2.1 39.6 1.0 O G:HOH420 2.1 40.1 1.0 OE1 G:GLU152 2.1 37.5 1.0 OAE G:DLU304 2.3 45.1 1.0 CD G:GLU152 2.4 37.0 1.0 CAZ G:DLU304 2.6 33.9 1.0 CAW G:DLU304 2.8 31.0 1.0 CG G:ASP64 3.2 39.9 1.0 OD1 G:ASP64 3.7 40.6 1.0 NZ G:LYS148 3.8 33.1 1.0 CG G:GLU152 3.9 26.6 1.0 MG G:MG301 3.9 47.5 1.0 CAX G:DLU304 4.0 27.5 1.0 ND2 G:ASN155 4.1 36.5 1.0 O G:HOH410 4.2 42.6 1.0 C5' L:DA21 4.3 18.4 0.5 CAY G:DLU304 4.4 28.1 1.0 CB G:ASP64 4.4 37.2 1.0 FAG G:DLU304 4.5 41.5 1.0 NAP G:DLU304 4.5 30.7 1.0 C2 L:DA21 4.6 14.9 0.5 CAR G:DLU304 4.7 32.4 1.0 CB G:GLU152 4.7 30.9 1.0 OAC G:DLU304 4.7 42.2 1.0 O G:CYS65 4.8 46.7 1.0 OP1 L:DA21 4.8 16.9 0.5 OP1 L:DA21 4.8 17.2 0.5 O3' L:DC20 4.9 15.3 1.0 N3 L:DA21 4.9 13.3 0.5 CA G:GLU152 5.0 23.2 1.0

M.Li, D.Oliveira Passos, Z.Shan, S.J.Smith, Q.Sun, A.Biswas, I.Choudhuri, T.S.Strutzenberg, A.Haldane, N.Deng, Z.Li, X.Z.Zhao, L.Briganti, M.Kvaratskhelia, T.R.Burke Jr., R.M.Levy, S.H.Hughes, R.Craigie, D.Lyumkis. Mechanisms of Hiv-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug-Resistant Variants. Sci Adv V. 9 G5953 2023.
ISSN: ESSN 2375-2548
PubMed: 37478179
DOI: 10.1126/SCIADV.ADG5953