Magnesium in PDB 8fnd: 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:

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

The binding sites of Magnesium atom in the Structure of E138K Hiv-1 Intasome with Dolutegravir Bound (pdb code 8fnd). 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: 8fnd:
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:68.6 occ:1.00 OAE A:DLU304 1.7 53.8 1.0 O A:HOH402 1.9 38.5 1.0 OAC A:DLU304 1.9 64.0 1.0 O A:HOH405 1.9 52.5 1.0 OD2 A:ASP116 2.0 48.3 1.0 OD1 A:ASP64 2.1 53.5 1.0 CAW A:DLU304 2.8 46.8 1.0 CAS A:DLU304 2.8 56.1 1.0 CG A:ASP64 3.0 48.9 1.0 CG A:ASP116 3.1 53.3 1.0 CAY A:DLU304 3.3 53.8 1.0 OD2 A:ASP64 3.4 55.4 1.0 OD1 A:ASP116 3.5 69.3 1.0 MG A:MG302 3.7 56.4 1.0 NBC A:DLU304 3.9 48.0 1.0 CAZ A:DLU304 4.1 45.5 1.0 OE2 A:GLU152 4.2 53.4 1.0 O A:HOH401 4.2 49.6 1.0 OAD A:DLU304 4.3 55.9 1.0 N1 F:DA21 4.4 64.4 0.5 CB A:ASP116 4.4 56.9 1.0 CBA A:DLU304 4.4 51.4 1.0 CB A:ASP64 4.4 46.2 1.0 O A:CYS65 4.4 69.5 1.0 N A:CYS65 4.6 55.6 1.0 C2 F:DA21 4.6 63.5 0.5 NBD A:DLU304 4.7 52.5 1.0 CA A:ASP64 4.8 47.9 1.0

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:56.4 occ:1.00 OAD A:DLU304 1.5 55.9 1.0 O A:HOH401 2.0 49.6 1.0 OE2 A:GLU152 2.0 53.4 1.0 OD2 A:ASP64 2.1 55.4 1.0 OE1 A:GLU152 2.1 64.8 1.0 OAE A:DLU304 2.3 53.8 1.0 CD A:GLU152 2.3 55.0 1.0 CAZ A:DLU304 2.4 45.5 1.0 CAW A:DLU304 2.7 46.8 1.0 CG A:ASP64 3.2 48.9 1.0 OD1 A:ASP64 3.7 53.5 1.0 MG A:MG301 3.7 68.6 1.0 ND2 A:ASN155 3.7 39.0 1.0 CAX A:DLU304 3.7 49.6 1.0 CG A:GLU152 3.9 46.5 1.0 O A:HOH402 4.2 38.5 1.0 C5' F:DA21 4.2 62.9 0.6 CAY A:DLU304 4.3 53.8 1.0 NAP A:DLU304 4.4 43.3 1.0 C2 F:DA21 4.4 63.5 0.5 CB A:ASP64 4.4 46.2 1.0 OP1 F:DA21 4.4 64.3 0.5 CAR A:DLU304 4.4 53.0 1.0 FAG A:DLU304 4.7 70.9 1.0 CB A:GLU152 4.7 44.5 1.0 N3 F:DA21 4.8 61.0 0.5 OP1 F:DA21 4.8 64.0 0.6 OD2 A:ASP116 4.8 48.3 1.0 O3' F:DC20 4.8 63.3 1.0 O A:CYS65 4.8 69.5 1.0 OAC A:DLU304 4.8 64.0 1.0 CAK A:DLU304 4.9 57.3 1.0 C2' F:DC20 5.0 59.4 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:68.6 occ:1.00 OAE G:DLU304 1.7 53.8 1.0 O G:HOH402 1.9 38.5 1.0 OAC G:DLU304 1.9 64.0 1.0 O G:HOH405 1.9 52.5 1.0 OD2 G:ASP116 2.0 48.3 1.0 OD1 G:ASP64 2.1 53.5 1.0 CAW G:DLU304 2.8 46.8 1.0 CAS G:DLU304 2.8 56.1 1.0 CG G:ASP64 3.0 48.9 1.0 CG G:ASP116 3.1 53.3 1.0 CAY G:DLU304 3.3 53.8 1.0 OD2 G:ASP64 3.4 55.4 1.0 OD1 G:ASP116 3.5 69.3 1.0 MG G:MG302 3.7 56.4 1.0 NBC G:DLU304 3.9 48.0 1.0 CAZ G:DLU304 4.1 45.5 1.0 OE2 G:GLU152 4.2 53.4 1.0 O G:HOH401 4.2 49.6 1.0 OAD G:DLU304 4.3 55.9 1.0 N1 L:DA21 4.4 64.4 0.5 CB G:ASP116 4.4 56.9 1.0 CB G:ASP64 4.4 46.2 1.0 CBA G:DLU304 4.4 51.4 1.0 O G:CYS65 4.4 69.5 1.0 N G:CYS65 4.6 55.6 1.0 C2 L:DA21 4.6 63.5 0.5 NBD G:DLU304 4.7 52.5 1.0 CA G:ASP64 4.8 47.9 1.0

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:56.4 occ:1.00 OAD G:DLU304 1.6 55.9 1.0 O G:HOH401 2.0 49.6 1.0 OE2 G:GLU152 2.0 53.4 1.0 OD2 G:ASP64 2.1 55.4 1.0 OE1 G:GLU152 2.1 64.8 1.0 OAE G:DLU304 2.3 53.8 1.0 CD G:GLU152 2.3 55.0 1.0 CAZ G:DLU304 2.4 45.5 1.0 CAW G:DLU304 2.7 46.8 1.0 CG G:ASP64 3.2 48.9 1.0 OD1 G:ASP64 3.7 53.5 1.0 MG G:MG301 3.7 68.6 1.0 ND2 G:ASN155 3.7 39.0 1.0 CAX G:DLU304 3.8 49.6 1.0 CG G:GLU152 3.9 46.5 1.0 O G:HOH402 4.2 38.5 1.0 C5' L:DA21 4.2 62.9 0.6 CAY G:DLU304 4.3 53.8 1.0 NAP G:DLU304 4.4 43.3 1.0 C2 L:DA21 4.4 63.5 0.5 CB G:ASP64 4.4 46.2 1.0 OP1 L:DA21 4.4 64.3 0.5 CAR G:DLU304 4.5 53.0 1.0 FAG G:DLU304 4.6 70.9 1.0 CB G:GLU152 4.7 44.5 1.0 N3 L:DA21 4.8 61.0 0.5 OP1 L:DA21 4.8 64.0 0.6 OD2 G:ASP116 4.8 48.3 1.0 O3' L:DC20 4.8 63.3 1.0 O G:CYS65 4.8 69.5 1.0 OAC G:DLU304 4.8 64.0 1.0 CAK G:DLU304 5.0 57.3 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