Fluorine in PDB 8w34: Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F

The structure of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F (pdb code 8w34). 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 Intasome Core Assembled with Wild-Type Integrase, 1F, PDB code: 8w34:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:38.1 occ:1.00 FAF A:DLU302 0.0 38.1 1.0 CAT A:DLU302 1.3 33.1 1.0 CAJ A:DLU302 2.3 32.9 1.0 CAH A:DLU302 2.3 34.6 1.0 N1 E:DG18 2.8 34.0 1.0 C6 E:DG18 2.9 35.1 1.0 C2 E:DG18 3.2 35.2 1.0 CG A:GLN146 3.3 35.4 1.0 CD A:GLN146 3.3 35.7 1.0 NE2 A:GLN146 3.3 38.3 1.0 O6 E:DG18 3.4 38.8 1.0 C5 E:DG18 3.4 32.9 1.0 CAU A:DLU302 3.5 37.1 1.0 CAI A:DLU302 3.5 37.1 1.0 C4 E:DG18 3.7 33.4 1.0 N3 E:DG18 3.7 35.2 1.0 N A:GLN146 3.8 34.1 1.0 CA A:GLN146 3.8 33.5 1.0 N2 E:DG18 3.9 35.5 1.0 OE1 A:GLN146 4.0 36.5 1.0 CAV A:DLU302 4.0 36.0 1.0 CB A:GLN146 4.1 34.9 1.0 C A:PRO145 4.2 32.9 1.0 N3 F:DC20 4.2 37.8 1.0 CB A:PRO145 4.3 32.9 1.0 N7 E:DG18 4.3 35.6 1.0 O A:PRO145 4.5 36.4 1.0 FAG A:DLU302 4.5 46.1 1.0 N4 F:DC20 4.6 37.0 1.0 C4 F:DC20 4.6 36.7 1.0 N9 E:DG18 4.7 34.6 1.0 CA A:PRO145 4.9 30.7 1.0 C2 F:DC20 4.9 38.2 1.0 C8 E:DG18 4.9 35.3 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:46.1 occ:1.00 FAG A:DLU302 0.0 46.1 1.0 CAU A:DLU302 1.2 37.1 1.0 CAV A:DLU302 2.2 36.0 1.0 CAJ A:DLU302 2.3 32.9 1.0 NAP A:DLU302 2.6 37.4 1.0 CAN A:DLU302 2.7 37.6 1.0 OE1 A:GLU152 3.0 37.3 1.0 C2' F:DC20 3.0 36.3 1.0 CD A:GLU152 3.2 36.6 1.0 OAD A:DLU302 3.3 42.3 1.0 CG A:GLU152 3.3 34.8 1.0 CB A:GLU152 3.4 30.8 1.0 CAT A:DLU302 3.5 33.1 1.0 CAI A:DLU302 3.5 37.1 1.0 N1 F:DC20 3.6 37.0 1.0 C1' F:DC20 3.7 35.8 1.0 CAR A:DLU302 3.7 38.4 1.0 C2 F:DC20 3.7 38.2 1.0 O2 F:DC20 3.9 41.3 1.0 CAH A:DLU302 4.0 34.6 1.0 CB A:PRO145 4.0 32.9 1.0 OE2 A:GLU152 4.0 36.9 1.0 C6 F:DC20 4.1 37.9 1.0 CAZ A:DLU302 4.2 39.5 1.0 N3 F:DC20 4.3 37.8 1.0 CAX A:DLU302 4.4 36.8 1.0 C3' F:DC20 4.5 37.7 1.0 OAB A:DLU302 4.5 40.6 1.0 FAF A:DLU302 4.5 38.1 1.0 CA A:GLU152 4.6 30.9 1.0 C5 F:DC20 4.6 37.1 1.0 MG A:MG304 4.7 40.7 1.0 C4 F:DC20 4.7 36.7 1.0 N2 E:DG18 4.8 35.5 1.0 CG A:PRO145 4.9 36.4 1.0 O3' F:DC20 5.0 41.1 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ I:F302 b:37.5 occ:1.00 FAF I:DLU302 0.0 37.5 1.0 CAT I:DLU302 1.3 32.3 1.0 CAJ I:DLU302 2.3 31.8 1.0 CAH I:DLU302 2.3 33.7 1.0 N1 N:DG18 2.9 32.9 1.0 C6 N:DG18 3.0 34.2 1.0 CD I:GLN146 3.3 34.5 1.0 C2 N:DG18 3.3 34.5 1.0 CG I:GLN146 3.3 34.2 1.0 NE2 I:GLN146 3.3 37.0 1.0 O6 N:DG18 3.4 37.1 1.0 C5 N:DG18 3.4 31.8 1.0 CAU I:DLU302 3.5 36.6 1.0 CAI I:DLU302 3.5 36.3 1.0 C4 N:DG18 3.7 32.2 1.0 N3 N:DG18 3.7 34.4 1.0 N I:GLN146 3.8 33.5 1.0 CA I:GLN146 3.8 33.1 1.0 OE1 I:GLN146 3.9 35.3 1.0 N2 N:DG18 3.9 34.6 1.0 CAV I:DLU302 4.0 35.8 1.0 CB I:GLN146 4.1 33.2 1.0 C I:PRO145 4.2 32.0 1.0 N3 O:DC20 4.2 37.0 1.0 N7 N:DG18 4.3 33.4 1.0 CB I:PRO145 4.3 32.8 1.0 O I:PRO145 4.5 36.4 1.0 FAG I:DLU302 4.5 45.1 1.0 N4 O:DC20 4.5 36.6 1.0 C4 O:DC20 4.6 36.1 1.0 N9 N:DG18 4.7 32.9 1.0 CA I:PRO145 4.9 30.4 1.0 C2 O:DC20 4.9 37.5 1.0 C8 N:DG18 4.9 33.4 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 Intasome Core Assembled with Wild-Type Integrase, 1F within 5.0Å range: probe atom residue distance (Å) B Occ I:F302 b:45.1 occ:1.00 FAG I:DLU302 0.0 45.1 1.0 CAU I:DLU302 1.2 36.6 1.0 CAV I:DLU302 2.3 35.8 1.0 CAJ I:DLU302 2.3 31.8 1.0 NAP I:DLU302 2.6 37.3 1.0 CAN I:DLU302 2.7 37.5 1.0 OE1 I:GLU152 3.0 37.9 1.0 C2' O:DC20 3.1 35.8 1.0 CD I:GLU152 3.2 36.6 1.0 CG I:GLU152 3.3 34.6 1.0 OAD I:DLU302 3.3 42.7 1.0 CB I:GLU152 3.4 31.5 1.0 CAT I:DLU302 3.5 32.3 1.0 CAI I:DLU302 3.5 36.3 1.0 N1 O:DC20 3.5 36.8 1.0 C2 O:DC20 3.7 37.5 1.0 C1' O:DC20 3.7 35.0 1.0 CAR I:DLU302 3.7 38.3 1.0 O2 O:DC20 3.8 40.4 1.0 CAH I:DLU302 4.0 33.7 1.0 OE2 I:GLU152 4.0 36.7 1.0 CB I:PRO145 4.0 32.8 1.0 C6 O:DC20 4.0 37.5 1.0 CAZ I:DLU302 4.2 39.5 1.0 N3 O:DC20 4.2 37.0 1.0 CAX I:DLU302 4.4 37.1 1.0 OAB I:DLU302 4.5 40.8 1.0 C3' O:DC20 4.5 36.3 1.0 FAF I:DLU302 4.5 37.5 1.0 CA I:GLU152 4.6 31.4 1.0 C5 O:DC20 4.6 36.3 1.0 C4 O:DC20 4.7 36.1 1.0 MG I:MG304 4.7 40.8 1.0 N2 N:DG18 4.8 34.6 1.0 CG I:PRO145 4.9 36.4 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