Magnesium in PDB 8fn7: Structure of Wt Hiv-1 Intasome Bound to Dolutegravir

The structure of Structure of Wt Hiv-1 Intasome Bound to Dolutegravir also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of Wt Hiv-1 Intasome Bound to Dolutegravir (pdb code 8fn7). 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 Wt Hiv-1 Intasome Bound to Dolutegravir, PDB code: 8fn7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Wt Hiv-1 Intasome Bound to Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Wt Hiv-1 Intasome Bound to Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:48.9 occ:1.00 OAE A:DLU304 1.7 36.9 1.0 O A:HOH405 1.9 36.5 1.0 O A:HOH402 2.0 34.8 1.0 OAC A:DLU304 2.1 42.1 1.0 OD1 A:ASP64 2.1 31.4 1.0 OD2 A:ASP116 2.1 40.5 1.0 CAW A:DLU304 3.0 28.8 1.0 CG A:ASP64 3.0 31.0 1.0 CAS A:DLU304 3.0 31.9 1.0 CG A:ASP116 3.2 32.9 1.0 OD2 A:ASP64 3.3 35.2 1.0 CAY A:DLU304 3.5 24.5 1.0 OD1 A:ASP116 3.6 44.1 1.0 MG A:MG302 3.7 41.4 1.0 O A:HOH403 3.9 31.3 1.0 O A:HOH432 4.0 41.5 1.0 O A:HOH407 4.0 31.1 1.0 NBC A:DLU304 4.1 27.7 1.0 O A:HOH401 4.2 35.0 1.0 CAZ A:DLU304 4.2 25.8 1.0 OE2 A:GLU152 4.2 34.1 1.0 N1 F:DA21 4.3 13.6 0.6 O A:CYS65 4.4 45.9 1.0 CB A:ASP64 4.4 30.9 1.0 OAD A:DLU304 4.4 30.6 1.0 CB A:ASP116 4.4 24.6 1.0 N A:CYS65 4.5 36.3 1.0 CBA A:DLU304 4.5 35.5 1.0 C2 F:DA21 4.6 13.3 0.6 CA A:ASP64 4.8 22.3 1.0 NBD A:DLU304 4.9 27.8 1.0 O A:HOH446 5.0 35.7 1.0

Magnesium binding site 2 out of 4 in the Structure of Wt Hiv-1 Intasome Bound to Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Wt Hiv-1 Intasome Bound to Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:41.4 occ:1.00 OAD A:DLU304 1.9 30.6 1.0 O A:HOH401 1.9 35.0 1.0 OE2 A:GLU152 2.0 34.1 1.0 OE1 A:GLU152 2.1 33.9 1.0 OD2 A:ASP64 2.1 35.2 1.0 CD A:GLU152 2.4 32.5 1.0 OAE A:DLU304 2.5 36.9 1.0 CAZ A:DLU304 2.7 25.8 1.0 CAW A:DLU304 3.0 28.8 1.0 CG A:ASP64 3.2 31.0 1.0 ND2 A:ASN155 3.6 36.4 1.0 MG A:MG301 3.7 48.9 1.0 OD1 A:ASP64 3.7 31.4 1.0 CG A:GLU152 3.9 23.1 1.0 O A:HOH403 4.0 31.3 1.0 CAX A:DLU304 4.1 27.3 1.0 O A:HOH402 4.1 34.8 1.0 C5' F:DA21 4.3 15.7 0.4 C2 F:DA21 4.4 13.3 0.6 OP1 F:DA21 4.4 12.5 0.6 CB A:ASP64 4.4 30.9 1.0 NAP A:DLU304 4.5 25.5 1.0 CAY A:DLU304 4.5 24.5 1.0 OP1 F:DA21 4.6 12.4 0.4 FAG A:DLU304 4.7 45.9 1.0 CB A:GLU152 4.7 23.7 1.0 O A:CYS65 4.7 45.9 1.0 N3 F:DA21 4.8 11.6 0.6 CAR A:DLU304 4.8 31.1 1.0 O3' F:DC20 4.8 13.2 1.0 CG A:ASN155 4.9 40.9 1.0 OAC A:DLU304 4.9 42.1 1.0 OD2 A:ASP116 4.9 40.5 1.0

Magnesium binding site 3 out of 4 in the Structure of Wt Hiv-1 Intasome Bound to Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Wt Hiv-1 Intasome Bound to Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:48.9 occ:1.00 OAE G:DLU304 1.7 36.9 1.0 O G:HOH405 1.9 36.5 1.0 O G:HOH403 2.0 34.8 1.0 OD1 G:ASP64 2.1 31.4 1.0 OAC G:DLU304 2.1 42.1 1.0 OD2 G:ASP116 2.1 40.5 1.0 CAW G:DLU304 3.0 28.8 1.0 CG G:ASP64 3.0 31.0 1.0 CAS G:DLU304 3.0 31.9 1.0 CG G:ASP116 3.2 32.9 1.0 OD2 G:ASP64 3.3 35.2 1.0 CAY G:DLU304 3.5 24.5 1.0 OD1 G:ASP116 3.6 44.1 1.0 MG G:MG302 3.7 41.4 1.0 O G:HOH402 3.9 31.3 1.0 O G:HOH432 4.0 41.5 1.0 O G:HOH407 4.0 31.1 1.0 NBC G:DLU304 4.1 27.7 1.0 O G:HOH401 4.2 35.0 1.0 CAZ G:DLU304 4.2 25.8 1.0 OE2 G:GLU152 4.2 34.1 1.0 N1 L:DA21 4.3 13.6 0.6 O G:CYS65 4.4 45.9 1.0 CB G:ASP64 4.4 30.9 1.0 OAD G:DLU304 4.4 30.6 1.0 CB G:ASP116 4.4 24.6 1.0 N G:CYS65 4.5 36.3 1.0 CBA G:DLU304 4.5 35.5 1.0 C2 L:DA21 4.6 13.3 0.6 CA G:ASP64 4.8 22.3 1.0 NBD G:DLU304 4.9 27.8 1.0 O G:HOH446 5.0 35.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Wt Hiv-1 Intasome Bound to Dolutegravir


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Wt Hiv-1 Intasome Bound to Dolutegravir within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:41.4 occ:1.00 OAD G:DLU304 1.9 30.6 1.0 O G:HOH401 1.9 35.0 1.0 OE2 G:GLU152 2.0 34.1 1.0 OE1 G:GLU152 2.1 33.9 1.0 OD2 G:ASP64 2.1 35.2 1.0 CD G:GLU152 2.4 32.5 1.0 OAE G:DLU304 2.5 36.9 1.0 CAZ G:DLU304 2.8 25.8 1.0 CAW G:DLU304 3.0 28.8 1.0 CG G:ASP64 3.2 31.0 1.0 ND2 G:ASN155 3.6 36.4 1.0 MG G:MG301 3.7 48.9 1.0 OD1 G:ASP64 3.7 31.4 1.0 CG G:GLU152 3.9 23.1 1.0 O G:HOH402 4.0 31.3 1.0 CAX G:DLU304 4.1 27.3 1.0 O G:HOH403 4.1 34.8 1.0 C5' L:DA21 4.3 15.7 0.4 C2 L:DA21 4.4 13.3 0.6 OP1 L:DA21 4.4 12.5 0.6 CB G:ASP64 4.4 30.9 1.0 NAP G:DLU304 4.5 25.5 1.0 CAY G:DLU304 4.5 24.5 1.0 OP1 L:DA21 4.6 12.4 0.4 FAG G:DLU304 4.7 45.9 1.0 CB G:GLU152 4.7 23.7 1.0 O G:CYS65 4.7 45.9 1.0 N3 L:DA21 4.8 11.6 0.6 O3' L:DC20 4.8 13.2 1.0 CAR G:DLU304 4.8 31.1 1.0 CG G:ASN155 4.9 40.9 1.0 OAC G:DLU304 4.9 42.1 1.0 OD2 G:ASP116 4.9 40.5 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