Fluorine in PDB 8w2r: Hiv-1 P5-in Intasome Core

The structure of Hiv-1 P5-in Intasome Core also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Hiv-1 P5-in Intasome Core (pdb code 8w2r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 P5-in Intasome Core, PDB code: 8w2r:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 P5-in Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:49.8 occ:1.00 FAF A:DLU304 0.0 49.8 1.0 CAT A:DLU304 1.3 43.0 1.0 CAJ A:DLU304 2.3 32.9 1.0 CAH A:DLU304 2.3 50.9 1.0 N1 E:DG18 2.8 30.7 1.0 NE2 A:GLN146 2.9 46.2 1.0 C6 E:DG18 2.9 37.8 1.0 O6 E:DG18 3.2 47.8 1.0 CG A:GLN146 3.3 36.9 1.0 C2 E:DG18 3.4 39.5 1.0 C5 E:DG18 3.4 41.0 1.0 CD A:GLN146 3.5 45.1 1.0 CAU A:DLU304 3.5 37.0 1.0 CAI A:DLU304 3.5 50.9 1.0 C4 E:DG18 3.8 39.8 1.0 N3 E:DG18 3.9 49.1 1.0 N A:GLN146 4.0 33.4 1.0 CAV A:DLU304 4.0 42.3 1.0 N2 E:DG18 4.0 47.5 1.0 CA A:GLN146 4.0 32.2 1.0 N3 F:DC20 4.2 58.0 1.0 CB A:GLN146 4.3 35.4 1.0 N7 E:DG18 4.3 51.1 1.0 CB A:PRO145 4.3 34.0 1.0 C A:PRO145 4.3 40.4 1.0 N4 F:DC20 4.5 56.8 1.0 FAG A:DLU304 4.5 56.5 1.0 OE1 A:GLN146 4.6 52.5 1.0 C4 F:DC20 4.6 52.5 1.0 O A:PRO145 4.7 54.9 1.0 N9 E:DG18 4.8 33.9 1.0 C2 F:DC20 4.9 60.1 1.0 CA A:PRO145 5.0 30.2 1.0 C8 E:DG18 5.0 42.8 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 P5-in Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:56.5 occ:1.00 FAG A:DLU304 0.0 56.5 1.0 CAU A:DLU304 1.2 37.0 1.0 CAJ A:DLU304 2.2 32.9 1.0 CAV A:DLU304 2.2 42.3 1.0 CAN A:DLU304 2.7 46.6 1.0 NAP A:DLU304 2.8 47.2 1.0 C2' F:DC20 3.1 54.5 1.0 OE1 A:GLU152 3.1 36.3 1.0 CD A:GLU152 3.3 39.7 1.0 CB A:GLU152 3.4 26.0 1.0 CG A:GLU152 3.4 32.4 1.0 CAT A:DLU304 3.5 43.0 1.0 CAI A:DLU304 3.5 50.9 1.0 N1 F:DC20 3.6 56.6 1.0 C2 F:DC20 3.6 60.1 1.0 O2 F:DC20 3.7 66.5 1.0 C1' F:DC20 3.7 58.1 1.0 OAD A:DLU304 3.8 47.4 1.0 CAR A:DLU304 3.9 47.1 1.0 CB A:PRO145 3.9 34.0 1.0 CAH A:DLU304 4.0 50.9 1.0 OE2 A:GLU152 4.1 36.8 1.0 C6 F:DC20 4.2 44.8 1.0 N3 F:DC20 4.2 58.0 1.0 C3' F:DC20 4.4 50.1 1.0 FAF A:DLU304 4.5 49.8 1.0 CAZ A:DLU304 4.5 49.4 1.0 CA A:GLU152 4.6 41.9 1.0 CAX A:DLU304 4.6 44.0 1.0 N2 E:DG18 4.7 47.5 1.0 OAB A:DLU304 4.7 48.0 1.0 C4 F:DC20 4.7 52.5 1.0 C5 F:DC20 4.7 45.3 1.0 CG A:PRO145 4.8 42.1 1.0 MG A:MG302 4.9 33.8 1.0 O3' F:DC20 5.0 60.5 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 P5-in Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:F304 b:48.2 occ:1.00 FAF I:DLU304 0.0 48.2 1.0 CAT I:DLU304 1.3 40.6 1.0 CAJ I:DLU304 2.3 32.2 1.0 CAH I:DLU304 2.3 48.8 1.0 NE2 I:GLN146 2.8 46.8 1.0 N1 N:DG18 2.9 31.3 1.0 C6 N:DG18 2.9 36.0 1.0 O6 N:DG18 3.2 45.0 1.0 CG I:GLN146 3.3 35.5 1.0 CD I:GLN146 3.4 43.9 1.0 C2 N:DG18 3.4 36.8 1.0 C5 N:DG18 3.4 37.7 1.0 CAU I:DLU304 3.5 37.0 1.0 CAI I:DLU304 3.5 50.2 1.0 C4 N:DG18 3.9 38.0 1.0 N3 N:DG18 3.9 45.6 1.0 N I:GLN146 4.0 32.0 1.0 CAV I:DLU304 4.0 41.5 1.0 CA I:GLN146 4.0 31.6 1.0 N2 N:DG18 4.1 46.2 1.0 N3 O:DC20 4.2 56.8 1.0 CB I:GLN146 4.3 34.2 1.0 N7 N:DG18 4.3 48.9 1.0 N4 O:DC20 4.3 55.2 1.0 C I:PRO145 4.3 35.4 1.0 CB I:PRO145 4.4 29.6 1.0 OE1 I:GLN146 4.4 52.8 1.0 C4 O:DC20 4.5 50.9 1.0 FAG I:DLU304 4.5 55.6 1.0 O I:PRO145 4.7 50.8 1.0 N9 N:DG18 4.8 31.5 1.0 C2 O:DC20 4.9 60.2 1.0 CA I:PRO145 5.0 25.4 1.0 C8 N:DG18 5.0 40.2 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 P5-in Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 P5-in Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:F304 b:55.6 occ:1.00 FAG I:DLU304 0.0 55.6 1.0 CAU I:DLU304 1.2 37.0 1.0 CAJ I:DLU304 2.2 32.2 1.0 CAV I:DLU304 2.2 41.5 1.0 CAN I:DLU304 2.7 46.0 1.0 NAP I:DLU304 2.8 47.1 1.0 C2' O:DC20 3.1 53.6 1.0 OE1 I:GLU152 3.1 36.3 1.0 CB I:GLU152 3.3 26.9 1.0 CD I:GLU152 3.3 37.4 1.0 CG I:GLU152 3.4 30.9 1.0 CAT I:DLU304 3.5 40.6 1.0 CAI I:DLU304 3.5 50.2 1.0 N1 O:DC20 3.5 56.6 1.0 C2 O:DC20 3.6 60.2 1.0 O2 O:DC20 3.7 66.8 1.0 C1' O:DC20 3.7 56.0 1.0 OAD I:DLU304 3.8 45.0 1.0 CAR I:DLU304 3.9 46.9 1.0 CAH I:DLU304 4.0 48.8 1.0 CB I:PRO145 4.0 29.6 1.0 C6 O:DC20 4.1 46.1 1.0 N3 O:DC20 4.1 56.8 1.0 OE2 I:GLU152 4.1 35.8 1.0 C3' O:DC20 4.5 50.3 1.0 FAF I:DLU304 4.5 48.2 1.0 CAZ I:DLU304 4.5 47.0 1.0 CA I:GLU152 4.5 48.3 1.0 C5 O:DC20 4.6 46.0 1.0 C4 O:DC20 4.6 50.9 1.0 CAX I:DLU304 4.6 42.8 1.0 OAB I:DLU304 4.6 46.5 1.0 N2 N:DG18 4.7 46.2 1.0 CG I:PRO145 4.9 40.7 1.0 MG I:MG302 4.9 32.3 1.0

M.Li, R.Yang, X.Chen, H.Wang, R.Ghirlando, E.K.Dimitriadis, R.Craigie. Hiv-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active For Concerted Dna Integration in Vitro. J.Mol.Biol. 68557 2024.
ISSN: ESSN 1089-8638
PubMed: 38582148
DOI: 10.1016/J.JMB.2024.168557