Magnesium in PDB 8fng: Structure of E138K Hiv-1 Intasome with Dolutegravir Bound

The structure of Structure of E138K 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 Hiv-1 Intasome with Dolutegravir Bound (pdb code 8fng). 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 Hiv-1 Intasome with Dolutegravir Bound, PDB code: 8fng:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of E138K 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 Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:0.0 occ:1.00 OD2 A:ASP116 2.1 0.0 1.0 OAC A:DLU304 2.1 12.2 1.0 OAE A:DLU304 2.1 0.7 1.0 OD1 A:ASP64 2.1 0.0 1.0 O A:HOH455 2.1 0.0 1.0 O A:HOH431 2.2 0.0 1.0 CG A:ASP116 3.1 0.0 1.0 CAS A:DLU304 3.1 0.0 1.0 CG A:ASP64 3.1 0.0 1.0 CAW A:DLU304 3.2 0.0 1.0 OD1 A:ASP116 3.3 0.0 1.0 OD2 A:ASP64 3.5 0.0 1.0 CAY A:DLU304 3.6 2.9 1.0 MG A:MG302 3.8 6.5 1.0 O A:HOH487 3.8 10.5 1.0 O A:HOH451 3.9 0.0 1.0 O A:HOH441 4.0 8.8 1.0 N1 F:DA21 4.1 6.0 0.4 O A:CYS65 4.1 0.0 1.0 NBC A:DLU304 4.2 5.1 1.0 O A:HOH438 4.2 1.2 1.0 N A:CYS65 4.3 6.9 1.0 O A:HOH549 4.4 10.2 1.0 CB A:ASP116 4.4 0.0 1.0 CB A:ASP64 4.4 0.0 1.0 OE2 A:GLU152 4.5 0.0 1.0 O F:HOH108 4.5 0.0 1.0 C2 F:DA21 4.5 3.1 0.4 O A:HOH404 4.6 0.5 1.0 CAZ A:DLU304 4.6 4.3 1.0 CBA A:DLU304 4.6 4.4 1.0 CA A:ASP64 4.7 0.0 1.0 CE2 A:PHE121 4.8 0.0 1.0 OAD A:DLU304 4.9 0.4 1.0 C6 F:DA21 5.0 6.0 0.4

Magnesium binding site 2 out of 4 in the Structure of E138K 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 Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:6.5 occ:1.00 O F:HOH108 2.0 0.0 1.0 OD2 A:ASP64 2.0 0.0 1.0 OE2 A:GLU152 2.0 0.0 1.0 OAD A:DLU304 2.2 0.4 1.0 OE1 A:GLU152 2.2 3.5 1.0 OAE A:DLU304 2.2 0.7 1.0 CD A:GLU152 2.4 0.0 1.0 CAZ A:DLU304 2.8 4.3 1.0 CAW A:DLU304 2.9 0.0 1.0 CG A:ASP64 3.1 0.0 1.0 OD1 A:ASP64 3.6 0.0 1.0 O A:HOH451 3.7 0.0 1.0 MG A:MG301 3.8 0.0 1.0 O A:HOH438 3.8 1.2 1.0 ND2 A:ASN155 3.9 3.1 1.0 CG A:GLU152 3.9 0.0 1.0 O A:HOH431 4.1 0.0 1.0 C5' F:DA21 4.2 2.3 0.6 C2 F:DA21 4.2 3.1 0.4 OP1 F:DA21 4.2 6.8 0.6 CAX A:DLU304 4.3 3.2 1.0 OP1 F:DA21 4.3 5.2 0.4 O A:CYS65 4.3 0.0 1.0 CB A:ASP64 4.4 0.0 1.0 CAY A:DLU304 4.4 2.9 1.0 OD2 A:ASP116 4.6 0.0 1.0 O3' F:DC20 4.6 10.0 1.0 N3 F:DA21 4.6 6.0 0.4 FAG A:DLU304 4.7 8.5 1.0 NAP A:DLU304 4.7 0.0 1.0 CB A:GLU152 4.8 0.0 1.0 OAC A:DLU304 4.9 12.2 1.0 N1 F:DA21 4.9 6.0 0.4 P F:DA21 4.9 0.0 0.6 C2' F:DC20 5.0 2.1 1.0

Magnesium binding site 3 out of 4 in the Structure of E138K 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 Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:0.0 occ:1.00 OD2 G:ASP116 2.1 0.0 1.0 OAC G:DLU304 2.1 12.2 1.0 OAE G:DLU304 2.1 0.7 1.0 OD1 G:ASP64 2.1 0.0 1.0 O G:HOH455 2.1 0.0 1.0 O G:HOH432 2.2 0.0 1.0 CG G:ASP116 3.1 0.0 1.0 CAS G:DLU304 3.1 0.0 1.0 CG G:ASP64 3.1 0.0 1.0 CAW G:DLU304 3.2 0.0 1.0 OD1 G:ASP116 3.3 0.0 1.0 OD2 G:ASP64 3.5 0.0 1.0 CAY G:DLU304 3.6 2.9 1.0 MG G:MG302 3.8 6.5 1.0 O G:HOH487 3.8 10.5 1.0 O G:HOH451 3.9 0.0 1.0 O G:HOH441 4.0 8.8 1.0 N1 L:DA21 4.1 6.0 0.4 O G:CYS65 4.1 0.0 1.0 NBC G:DLU304 4.2 5.1 1.0 O G:HOH438 4.2 1.2 1.0 N G:CYS65 4.3 6.9 1.0 O G:HOH549 4.4 10.2 1.0 CB G:ASP116 4.4 0.0 1.0 CB G:ASP64 4.4 0.0 1.0 OE2 G:GLU152 4.5 0.0 1.0 O L:HOH108 4.5 0.0 1.0 C2 L:DA21 4.5 3.1 0.4 O G:HOH404 4.6 0.5 1.0 CAZ G:DLU304 4.6 4.3 1.0 CBA G:DLU304 4.6 4.4 1.0 CA G:ASP64 4.7 0.0 1.0 CE2 G:PHE121 4.8 0.0 1.0 OAD G:DLU304 4.9 0.4 1.0 C6 L:DA21 5.0 6.0 0.4

Magnesium binding site 4 out of 4 in the Structure of E138K 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 Hiv-1 Intasome with Dolutegravir Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:6.5 occ:1.00 O L:HOH108 2.0 0.0 1.0 OD2 G:ASP64 2.0 0.0 1.0 OE2 G:GLU152 2.0 0.0 1.0 OAD G:DLU304 2.2 0.4 1.0 OE1 G:GLU152 2.2 3.5 1.0 OAE G:DLU304 2.2 0.7 1.0 CD G:GLU152 2.4 0.0 1.0 CAZ G:DLU304 2.8 4.3 1.0 CAW G:DLU304 2.9 0.0 1.0 CG G:ASP64 3.1 0.0 1.0 OD1 G:ASP64 3.6 0.0 1.0 O G:HOH451 3.7 0.0 1.0 MG G:MG301 3.8 0.0 1.0 O G:HOH438 3.8 1.2 1.0 ND2 G:ASN155 3.9 3.1 1.0 CG G:GLU152 3.9 0.0 1.0 O G:HOH432 4.1 0.0 1.0 C5' L:DA21 4.2 2.3 0.6 C2 L:DA21 4.2 3.1 0.4 OP1 L:DA21 4.2 6.8 0.6 CAX G:DLU304 4.3 3.2 1.0 OP1 L:DA21 4.3 5.2 0.4 O G:CYS65 4.3 0.0 1.0 CB G:ASP64 4.4 0.0 1.0 CAY G:DLU304 4.4 2.9 1.0 OD2 G:ASP116 4.6 0.0 1.0 O3' L:DC20 4.6 10.0 1.0 N3 L:DA21 4.6 6.0 0.4 FAG G:DLU304 4.7 8.5 1.0 NAP G:DLU304 4.7 0.0 1.0 CB G:GLU152 4.8 0.0 1.0 OAC G:DLU304 4.9 12.2 1.0 N1 L:DA21 4.9 6.0 0.4 P L:DA21 4.9 0.0 0.6 C2' L:DC20 5.0 2.1 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