Fluorine in PDB 8w09: Hiv-1 Wild-Type Intasome Core

The structure of Hiv-1 Wild-Type 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 Wild-Type Intasome Core (pdb code 8w09). 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 Wild-Type Intasome Core, PDB code: 8w09:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Wild-Type 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 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:41.9 occ:1.00 FAF A:DLU304 0.0 41.9 1.0 CAT A:DLU304 1.3 33.1 1.0 CAJ A:DLU304 2.3 33.0 1.0 CAH A:DLU304 2.3 27.7 1.0 N1 E:DG18 2.7 23.7 1.0 C6 E:DG18 3.0 22.0 1.0 C2 E:DG18 3.0 26.6 1.0 CG A:GLN146 3.4 28.1 1.0 C5 E:DG18 3.5 19.8 1.0 O6 E:DG18 3.5 28.3 1.0 CAU A:DLU304 3.5 32.9 1.0 N3 E:DG18 3.5 30.8 1.0 CAI A:DLU304 3.5 30.4 1.0 N2 E:DG18 3.6 29.0 1.0 C4 E:DG18 3.6 22.6 1.0 CD A:GLN146 3.7 30.3 1.0 CA A:GLN146 3.7 27.6 1.0 N A:GLN146 3.7 30.4 1.0 NE2 A:GLN146 3.9 31.4 1.0 N3 F:DC20 4.0 30.3 1.0 CAV A:DLU304 4.0 29.3 1.0 C A:PRO145 4.0 29.6 1.0 CB A:GLN146 4.1 25.0 1.0 O A:PRO145 4.3 38.2 1.0 OE1 A:GLN146 4.3 35.4 1.0 CB A:PRO145 4.3 22.3 1.0 N7 E:DG18 4.4 31.1 1.0 N4 F:DC20 4.5 33.0 1.0 FAG A:DLU304 4.5 38.5 1.0 C4 F:DC20 4.5 28.1 1.0 C2 F:DC20 4.7 32.3 1.0 N9 E:DG18 4.7 21.8 1.0 O2 F:DC20 4.7 38.9 1.0 CA A:PRO145 4.8 20.0 1.0 C A:GLN146 5.0 30.2 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 Wild-Type 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 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:38.5 occ:1.00 FAG A:DLU304 0.0 38.5 1.0 CAU A:DLU304 1.2 32.9 1.0 CAV A:DLU304 2.2 29.3 1.0 CAJ A:DLU304 2.3 33.0 1.0 NAP A:DLU304 2.5 28.2 1.0 CAN A:DLU304 2.7 29.0 1.0 OE1 A:GLU152 2.9 39.0 1.0 CD A:GLU152 3.0 30.9 1.0 OAD A:DLU304 3.1 38.7 1.0 CG A:GLU152 3.1 30.1 1.0 CB A:GLU152 3.3 27.0 1.0 CAR A:DLU304 3.4 28.2 1.0 C2' F:DC20 3.5 28.0 1.0 CAI A:DLU304 3.5 30.4 1.0 CAT A:DLU304 3.5 33.1 1.0 OE2 A:GLU152 3.7 23.6 1.0 CB A:PRO145 3.9 22.3 1.0 CAZ A:DLU304 3.9 34.0 1.0 CAH A:DLU304 4.0 27.7 1.0 C2 F:DC20 4.1 32.3 1.0 CAX A:DLU304 4.1 26.4 1.0 O2 F:DC20 4.1 38.9 1.0 N1 F:DC20 4.1 32.3 1.0 OAB A:DLU304 4.2 30.4 1.0 C1' F:DC20 4.3 32.1 1.0 MG A:MG302 4.4 41.6 1.0 FAF A:DLU304 4.5 41.9 1.0 CA A:GLU152 4.5 26.7 1.0 N3 F:DC20 4.6 30.3 1.0 C6 F:DC20 4.7 30.8 1.0 C3' F:DC20 4.8 27.2 1.0 CG A:PRO145 4.8 30.7 1.0 O4' F:DA21 4.8 34.4 0.3 O A:PRO145 4.9 38.2 1.0 CA A:PRO145 5.0 20.0 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 Wild-Type 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 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:F304 b:37.6 occ:1.00 FAF I:DLU304 0.0 37.6 1.0 CAT I:DLU304 1.3 30.2 1.0 CAJ I:DLU304 2.3 28.7 1.0 CAH I:DLU304 2.3 27.1 1.0 N1 N:DG18 2.7 20.0 1.0 C2 N:DG18 3.0 24.9 1.0 C6 N:DG18 3.0 19.0 1.0 CG I:GLN146 3.5 26.9 1.0 CAU I:DLU304 3.5 29.4 1.0 C5 N:DG18 3.5 16.9 1.0 N2 N:DG18 3.5 26.5 1.0 CAI I:DLU304 3.5 28.3 1.0 N3 N:DG18 3.5 30.0 1.0 O6 N:DG18 3.5 28.1 1.0 C4 N:DG18 3.7 20.3 1.0 CA I:GLN146 3.7 24.8 1.0 CD I:GLN146 3.8 27.4 1.0 N I:GLN146 3.8 28.0 1.0 NE2 I:GLN146 3.9 29.9 1.0 N3 O:DC20 3.9 30.5 1.0 CAV I:DLU304 4.0 26.2 1.0 C I:PRO145 4.0 24.6 1.0 CB I:GLN146 4.2 23.5 1.0 O I:PRO145 4.2 33.1 1.0 CB I:PRO145 4.3 17.8 1.0 OE1 I:GLN146 4.4 31.6 1.0 N4 O:DC20 4.5 30.7 1.0 C4 O:DC20 4.5 26.7 1.0 N7 N:DG18 4.5 27.9 1.0 FAG I:DLU304 4.5 38.0 1.0 C2 O:DC20 4.6 31.6 1.0 O2 O:DC20 4.7 35.6 1.0 N9 N:DG18 4.7 18.6 1.0 CA I:PRO145 4.8 11.1 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 Wild-Type 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 Wild-Type Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:F304 b:38.0 occ:1.00 FAG I:DLU304 0.0 38.0 1.0 CAU I:DLU304 1.2 29.4 1.0 CAV I:DLU304 2.2 26.2 1.0 CAJ I:DLU304 2.3 28.7 1.0 NAP I:DLU304 2.5 25.8 1.0 CAN I:DLU304 2.7 26.5 1.0 CD I:GLU152 2.9 27.6 1.0 OE1 I:GLU152 3.0 37.3 1.0 OAD I:DLU304 3.0 35.3 1.0 CG I:GLU152 3.1 22.5 1.0 CB I:GLU152 3.3 22.2 1.0 CAR I:DLU304 3.4 26.1 1.0 C2' O:DC20 3.5 29.2 1.0 CAI I:DLU304 3.5 28.3 1.0 CAT I:DLU304 3.5 30.2 1.0 OE2 I:GLU152 3.6 21.1 1.0 CAZ I:DLU304 3.9 31.8 1.0 CB I:PRO145 3.9 17.8 1.0 CAH I:DLU304 4.0 27.1 1.0 CAX I:DLU304 4.0 24.0 1.0 C2 O:DC20 4.1 31.6 1.0 OAB I:DLU304 4.1 28.1 1.0 O2 O:DC20 4.1 35.6 1.0 N1 O:DC20 4.2 30.4 1.0 C1' O:DC20 4.3 29.6 1.0 MG I:MG302 4.4 39.5 1.0 FAF I:DLU304 4.5 37.6 1.0 CA I:GLU152 4.6 26.8 1.0 N3 O:DC20 4.7 30.5 1.0 C6 O:DC20 4.7 30.6 1.0 O4' O:DA21 4.8 31.5 0.3 C3' O:DC20 4.8 26.3 1.0 CG I:PRO145 4.9 26.6 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