Fluorine 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
Magnesium	(Mg)	4 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of E138K Hiv-1 Intasome with Dolutegravir Bound, PDB code: 8fnd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine 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 Fluorine with other atoms in the F 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:F304 b:63.2 occ:1.00 FAF A:DLU304 0.0 63.2 1.0 CAT A:DLU304 1.3 47.9 1.0 CG A:GLN146 2.3 46.0 1.0 CAH A:DLU304 2.3 50.7 1.0 CAJ A:DLU304 2.4 45.6 1.0 CD A:GLN146 2.5 54.7 1.0 CA A:GLN146 2.6 41.9 1.0 N A:GLN146 2.7 48.2 1.0 CB A:GLN146 2.9 45.7 1.0 NE2 A:GLN146 2.9 61.0 1.0 OE1 A:GLN146 3.1 61.6 1.0 C A:PRO145 3.3 36.1 1.0 CAU A:DLU304 3.6 52.9 1.0 CAI A:DLU304 3.6 58.2 1.0 C5 E:DG18 3.6 52.1 1.0 C6 E:DG18 3.6 59.9 1.0 N1 E:DG18 3.6 56.6 1.0 C4 E:DG18 3.7 50.7 1.0 C2 E:DG18 3.7 48.8 1.0 N3 E:DG18 3.8 51.8 1.0 C A:GLN146 4.1 43.9 1.0 CAV A:DLU304 4.1 50.0 1.0 O6 E:DG18 4.2 63.9 1.0 CB A:PRO145 4.2 55.3 1.0 CA A:PRO145 4.3 48.3 1.0 N7 E:DG18 4.3 58.6 1.0 N9 E:DG18 4.4 48.8 1.0 N2 E:DG18 4.4 51.2 1.0 O A:HOH412 4.6 62.7 1.0 C8 E:DG18 4.6 56.0 1.0 O A:GLN146 4.6 56.2 1.0 N A:PRO145 4.7 40.3 1.0 CD A:PRO145 4.7 42.2 1.0 FAG A:DLU304 4.7 70.9 1.0 CG A:PRO145 4.8 46.9 1.0 O4' E:DG18 4.8 50.2 1.0 N A:SER147 5.0 33.2 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F304 b:70.9 occ:1.00 FAG A:DLU304 0.0 70.9 1.0 CAU A:DLU304 1.4 52.9 1.0 CAJ A:DLU304 2.3 45.6 1.0 CAV A:DLU304 2.4 50.0 1.0 CG A:GLU152 2.6 46.5 1.0 CB A:GLU152 2.6 44.5 1.0 NAP A:DLU304 2.8 43.3 1.0 CAN A:DLU304 2.8 51.5 1.0 CD A:GLU152 3.1 55.0 1.0 OE1 A:GLU152 3.1 64.8 1.0 O2 F:DC20 3.4 64.2 1.0 C2 F:DC20 3.6 63.8 1.0 CB A:PRO145 3.6 55.3 1.0 CAT A:DLU304 3.6 47.9 1.0 CAI A:DLU304 3.6 58.2 1.0 C2' F:DC20 3.7 59.4 1.0 N1 F:DC20 3.9 59.6 1.0 CA A:GLU152 4.0 48.7 1.0 OE2 A:GLU152 4.0 53.4 1.0 C1' F:DC20 4.0 69.8 1.0 CAH A:DLU304 4.1 50.7 1.0 N3 F:DC20 4.1 62.5 1.0 N2 E:DG18 4.1 51.2 1.0 CAR A:DLU304 4.2 53.0 1.0 OAD A:DLU304 4.3 55.9 1.0 CG A:PRO145 4.6 46.9 1.0 C A:PRO145 4.6 36.1 1.0 C6 F:DC20 4.6 52.4 1.0 C A:GLU152 4.6 45.0 1.0 CA A:PRO145 4.7 48.3 1.0 MG A:MG302 4.7 56.4 1.0 FAF A:DLU304 4.7 63.2 1.0 C2 E:DG18 4.8 48.8 1.0 C4 F:DC20 4.8 56.6 1.0 N1 E:DG18 4.9 56.6 1.0 CAZ A:DLU304 4.9 45.5 1.0 CAX A:DLU304 5.0 49.6 1.0 O A:GLU152 5.0 55.5 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F304 b:63.2 occ:1.00 FAF G:DLU304 0.0 63.2 1.0 CAT G:DLU304 1.3 47.9 1.0 CAH G:DLU304 2.3 50.7 1.0 CG G:GLN146 2.3 46.0 1.0 CAJ G:DLU304 2.4 45.6 1.0 CD G:GLN146 2.5 54.7 1.0 CA G:GLN146 2.7 41.9 1.0 N G:GLN146 2.7 48.2 1.0 NE2 G:GLN146 3.0 61.0 1.0 CB G:GLN146 3.0 45.7 1.0 OE1 G:GLN146 3.1 61.6 1.0 C G:PRO145 3.3 36.1 1.0 CAU G:DLU304 3.6 52.9 1.0 CAI G:DLU304 3.6 58.2 1.0 C6 K:DG18 3.6 59.9 1.0 N1 K:DG18 3.6 56.6 1.0 C5 K:DG18 3.6 52.1 1.0 C4 K:DG18 3.7 50.7 1.0 C2 K:DG18 3.7 48.8 1.0 N3 K:DG18 3.8 51.8 1.0 CAV G:DLU304 4.1 50.0 1.0 C G:GLN146 4.1 43.9 1.0 O6 K:DG18 4.2 63.9 1.0 CB G:PRO145 4.2 55.3 1.0 CA G:PRO145 4.2 48.3 1.0 N7 K:DG18 4.3 58.6 1.0 N9 K:DG18 4.4 48.8 1.0 N2 K:DG18 4.4 51.2 1.0 O G:HOH412 4.6 62.7 1.0 N G:PRO145 4.7 40.3 1.0 CD G:PRO145 4.7 42.2 1.0 C8 K:DG18 4.7 56.0 1.0 O G:GLN146 4.7 56.2 1.0 FAG G:DLU304 4.7 70.9 1.0 CG G:PRO145 4.8 46.9 1.0 O4' K:DG18 4.9 50.2 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F304 b:70.9 occ:1.00 FAG G:DLU304 0.0 70.9 1.0 CAU G:DLU304 1.4 52.9 1.0 CAJ G:DLU304 2.3 45.6 1.0 CAV G:DLU304 2.4 50.0 1.0 CG G:GLU152 2.6 46.5 1.0 CB G:GLU152 2.6 44.5 1.0 NAP G:DLU304 2.8 43.3 1.0 CAN G:DLU304 2.8 51.5 1.0 OE1 G:GLU152 3.0 64.8 1.0 CD G:GLU152 3.0 55.0 1.0 O2 L:DC20 3.4 64.2 1.0 C2 L:DC20 3.6 63.8 1.0 CAT G:DLU304 3.6 47.9 1.0 CB G:PRO145 3.6 55.3 1.0 CAI G:DLU304 3.6 58.2 1.0 C2' L:DC20 3.7 59.4 1.0 N1 L:DC20 3.8 59.6 1.0 C1' L:DC20 4.0 69.8 1.0 CA G:GLU152 4.0 48.7 1.0 OE2 G:GLU152 4.0 53.4 1.0 CAH G:DLU304 4.1 50.7 1.0 N3 L:DC20 4.1 62.5 1.0 N2 K:DG18 4.2 51.2 1.0 CAR G:DLU304 4.2 53.0 1.0 OAD G:DLU304 4.2 55.9 1.0 C6 L:DC20 4.6 52.4 1.0 CG G:PRO145 4.6 46.9 1.0 C G:GLU152 4.6 45.0 1.0 MG G:MG302 4.6 56.4 1.0 C G:PRO145 4.7 36.1 1.0 CA G:PRO145 4.7 48.3 1.0 FAF G:DLU304 4.7 63.2 1.0 C4 L:DC20 4.8 56.6 1.0 C2 K:DG18 4.9 48.8 1.0 CAZ G:DLU304 4.9 45.5 1.0 N1 K:DG18 4.9 56.6 1.0 O G:GLU152 5.0 55.5 1.0 CAX G:DLU304 5.0 49.6 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