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

Other elements in 8w34:

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

Fluorine Binding Sites:

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 8w34

Go back to Fluorine Binding Sites List in 8w34
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 8w34

Go back to Fluorine Binding Sites List in 8w34
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 8w34

Go back to Fluorine Binding Sites List in 8w34
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 8w34

Go back to Fluorine Binding Sites List in 8w34
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

Reference:

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
Page generated: Wed Jul 16 09:51:36 2025

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