Magnesium in PDB 8fnj: Structure of E138K/G140A Hiv-1 Intasome with Dolutegravir Bound

The structure of Structure of E138K/G140A Hiv-1 Intasome with Dolutegravir Bound also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of E138K/G140A Hiv-1 Intasome with Dolutegravir Bound (pdb code 8fnj). 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 E138K/G140A Hiv-1 Intasome with Dolutegravir Bound, PDB code: 8fnj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of E138K/G140A 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 E138K/G140A Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:54.8 occ:1.00 O A:HOH401 1.5 45.4 1.0 O A:HOH418 1.9 39.8 1.0 OAE A:DLU304 2.0 45.0 1.0 OAC A:DLU304 2.1 38.1 1.0 OD2 A:ASP116 2.1 47.8 1.0 OD1 A:ASP64 2.1 42.0 1.0 CAS A:DLU304 3.1 35.5 1.0 CG A:ASP64 3.1 37.2 1.0 CG A:ASP116 3.1 42.2 1.0 CAW A:DLU304 3.2 28.6 1.0 OD2 A:ASP64 3.4 39.4 1.0 OD1 A:ASP116 3.5 53.6 1.0 CAY A:DLU304 3.7 38.0 1.0 MG A:MG302 3.9 38.0 1.0 O A:HOH411 4.0 49.6 1.0 NBC A:DLU304 4.2 41.1 1.0 O A:HOH412 4.3 42.0 1.0 O A:CYS65 4.3 48.9 1.0 N A:CYS65 4.3 45.5 1.0 N1 F:DA21 4.3 29.3 0.6 CB A:ASP64 4.4 37.3 1.0 CB A:ASP116 4.4 33.9 1.0 CAZ A:DLU304 4.5 39.2 1.0 CBA A:DLU304 4.5 43.6 1.0 C2 F:DA21 4.6 29.4 0.6 OE2 A:GLU152 4.6 39.4 1.0 O F:HOH103 4.6 40.4 1.0 CA A:ASP64 4.7 30.6 1.0 OAD A:DLU304 4.8 52.5 1.0 CE2 A:PHE121 4.8 48.0 1.0

Magnesium binding site 2 out of 4 in the Structure of E138K/G140A 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 E138K/G140A Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:38.0 occ:1.00 OE1 A:GLU152 2.1 42.0 1.0 OD2 A:ASP64 2.1 39.4 1.0 OE2 A:GLU152 2.2 39.4 1.0 OAD A:DLU304 2.2 52.5 1.0 O F:HOH103 2.2 40.4 1.0 CD A:GLU152 2.4 39.9 1.0 OAE A:DLU304 2.5 45.0 1.0 CAZ A:DLU304 3.0 39.2 1.0 CAW A:DLU304 3.1 28.6 1.0 CG A:ASP64 3.1 37.2 1.0 OD1 A:ASP64 3.6 42.0 1.0 O A:HOH411 3.8 49.6 1.0 ND2 A:ASN155 3.8 36.2 1.0 MG A:MG301 3.9 54.8 1.0 CG A:GLU152 3.9 33.4 1.0 O A:HOH418 4.0 39.8 1.0 C5' F:DA21 4.2 31.1 0.4 OP1 F:DA21 4.2 31.1 0.6 OP1 F:DA21 4.3 32.2 0.4 O A:CYS65 4.3 48.9 1.0 CAX A:DLU304 4.3 27.7 1.0 CB A:ASP64 4.4 37.3 1.0 FAG A:DLU304 4.5 54.5 1.0 C2 F:DA21 4.6 29.4 0.6 CAY A:DLU304 4.6 38.0 1.0 NAP A:DLU304 4.7 31.0 1.0 CB A:GLU152 4.8 26.4 1.0 O3' F:DC20 4.8 31.1 1.0 OD2 A:ASP116 4.8 47.8 1.0 O5' F:DA21 4.9 31.4 0.4 N3 F:DA21 4.9 28.9 0.6 P F:DA21 5.0 30.4 0.4 C5' F:DA21 5.0 31.3 0.6 CA A:GLU152 5.0 31.2 1.0 OAC A:DLU304 5.0 38.1 1.0

Magnesium binding site 3 out of 4 in the Structure of E138K/G140A 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 E138K/G140A Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:54.8 occ:1.00 O G:HOH401 1.5 45.4 1.0 O G:HOH418 1.9 39.8 1.0 OAE G:DLU304 2.0 45.0 1.0 OAC G:DLU304 2.1 38.1 1.0 OD2 G:ASP116 2.1 47.8 1.0 OD1 G:ASP64 2.1 42.0 1.0 CAS G:DLU304 3.1 35.5 1.0 CG G:ASP64 3.1 37.2 1.0 CG G:ASP116 3.1 42.2 1.0 CAW G:DLU304 3.2 28.6 1.0 OD2 G:ASP64 3.4 39.4 1.0 OD1 G:ASP116 3.5 53.6 1.0 CAY G:DLU304 3.7 38.0 1.0 MG G:MG302 3.9 38.0 1.0 O G:HOH411 4.0 49.6 1.0 NBC G:DLU304 4.2 41.1 1.0 O G:CYS65 4.3 48.9 1.0 O G:HOH412 4.3 42.0 1.0 N G:CYS65 4.3 45.5 1.0 N1 L:DA21 4.3 29.3 0.6 CB G:ASP64 4.4 37.3 1.0 CB G:ASP116 4.4 33.9 1.0 CAZ G:DLU304 4.5 39.2 1.0 CBA G:DLU304 4.5 43.6 1.0 C2 L:DA21 4.6 29.4 0.6 OE2 G:GLU152 4.6 39.4 1.0 O L:HOH103 4.6 40.4 1.0 CA G:ASP64 4.7 30.6 1.0 OAD G:DLU304 4.8 52.5 1.0 CE2 G:PHE121 4.8 48.0 1.0

Magnesium binding site 4 out of 4 in the Structure of E138K/G140A 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 E138K/G140A Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:38.0 occ:1.00 OE1 G:GLU152 2.1 42.0 1.0 OD2 G:ASP64 2.1 39.4 1.0 OE2 G:GLU152 2.2 39.4 1.0 OAD G:DLU304 2.2 52.5 1.0 O L:HOH103 2.2 40.4 1.0 CD G:GLU152 2.4 39.9 1.0 OAE G:DLU304 2.5 45.0 1.0 CAZ G:DLU304 3.0 39.2 1.0 CAW G:DLU304 3.1 28.6 1.0 CG G:ASP64 3.1 37.2 1.0 OD1 G:ASP64 3.6 42.0 1.0 O G:HOH411 3.8 49.6 1.0 ND2 G:ASN155 3.8 36.2 1.0 MG G:MG301 3.9 54.8 1.0 CG G:GLU152 3.9 33.4 1.0 O G:HOH418 4.0 39.8 1.0 C5' L:DA21 4.2 31.1 0.4 OP1 L:DA21 4.2 31.1 0.6 OP1 L:DA21 4.3 32.2 0.4 O G:CYS65 4.3 48.9 1.0 CAX G:DLU304 4.3 27.7 1.0 CB G:ASP64 4.4 37.3 1.0 FAG G:DLU304 4.5 54.5 1.0 C2 L:DA21 4.6 29.4 0.6 CAY G:DLU304 4.6 38.0 1.0 NAP G:DLU304 4.7 31.0 1.0 CB G:GLU152 4.8 26.4 1.0 O3' L:DC20 4.8 31.1 1.0 OD2 G:ASP116 4.8 47.8 1.0 O5' L:DA21 4.9 31.4 0.4 N3 L:DA21 4.9 28.9 0.6 P L:DA21 5.0 30.4 0.4 C5' L:DA21 5.0 31.3 0.6 CA G:GLU152 5.0 31.2 1.0 OAC G:DLU304 5.0 38.1 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