Fluorine in PDB 9c9m: Hiv-1 Intasome Core Bound with Dtg

The structure of Hiv-1 Intasome Core Bound with Dtg also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Hiv-1 Intasome Core Bound with Dtg (pdb code 9c9m). 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 Bound with Dtg, PDB code: 9c9m:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:6.2 occ:1.00 FAF F:DLU101 0.0 6.2 1.0 CAT F:DLU101 1.3 6.0 1.0 CAJ F:DLU101 2.3 3.7 1.0 CAH F:DLU101 2.3 3.7 1.0 N1 E:DG18 2.9 4.7 1.0 C6 E:DG18 3.0 3.0 1.0 C2 E:DG18 3.3 2.7 1.0 CG A:GLN146 3.3 4.3 1.0 C5 E:DG18 3.3 3.1 1.0 O A:HOH411 3.4 7.7 1.0 O6 E:DG18 3.5 5.2 1.0 NE2 A:GLN146 3.5 4.9 1.0 CD A:GLN146 3.5 5.8 1.0 CAU F:DLU101 3.5 4.2 1.0 CAI F:DLU101 3.5 4.6 1.0 C4 E:DG18 3.6 2.7 1.0 N3 E:DG18 3.6 2.3 1.0 N A:GLN146 3.8 4.8 1.0 CA A:GLN146 3.8 3.2 1.0 N2 E:DG18 3.9 4.5 1.0 CAV F:DLU101 4.0 5.8 1.0 CB A:GLN146 4.1 5.4 1.0 C A:PRO145 4.2 3.6 1.0 N7 E:DG18 4.2 3.6 1.0 OE1 A:GLN146 4.2 8.4 1.0 N3 F:DC20 4.2 5.6 1.0 CB A:PRO145 4.4 6.2 1.0 O A:PRO145 4.5 4.2 1.0 FAG F:DLU101 4.5 8.7 1.0 N4 F:DC20 4.5 5.0 1.0 N9 E:DG18 4.5 2.4 1.0 C4 F:DC20 4.6 4.5 1.0 C8 E:DG18 4.8 3.9 1.0 C2 F:DC20 4.9 5.4 1.0 CA A:PRO145 4.9 3.8 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:8.7 occ:1.00 FAG F:DLU101 0.0 8.7 1.0 CAU F:DLU101 1.2 4.2 1.0 CAJ F:DLU101 2.3 3.7 1.0 CAV F:DLU101 2.3 5.8 1.0 NAP F:DLU101 2.7 8.5 1.0 CAN F:DLU101 2.7 5.8 1.0 OE1 A:GLU152 3.1 9.6 1.0 CG A:GLU152 3.1 2.9 1.0 C2' F:DC20 3.2 6.9 1.0 CD A:GLU152 3.3 5.9 1.0 CB A:GLU152 3.4 3.1 1.0 OAD F:DLU101 3.5 10.0 1.0 CAT F:DLU101 3.5 6.0 1.0 CAI F:DLU101 3.5 4.6 1.0 N1 F:DC20 3.7 7.5 1.0 C2 F:DC20 3.7 5.4 1.0 CB A:PRO145 3.8 6.2 1.0 CAR F:DLU101 3.8 6.5 1.0 C1' F:DC20 3.9 5.8 1.0 O2 F:DC20 3.9 4.7 1.0 CAH F:DLU101 4.0 3.7 1.0 OE2 A:GLU152 4.1 7.0 1.0 C6 F:DC20 4.2 6.1 1.0 N3 F:DC20 4.3 5.6 1.0 CAZ F:DLU101 4.3 6.7 1.0 CAX F:DLU101 4.5 7.2 1.0 FAF F:DLU101 4.5 6.2 1.0 CA A:GLU152 4.6 2.3 1.0 C3' F:DC20 4.6 8.7 1.0 C5 F:DC20 4.6 4.8 1.0 C4 F:DC20 4.7 4.5 1.0 OAB F:DLU101 4.7 14.4 1.0 CG A:PRO145 4.7 7.2 1.0 MG A:MG302 4.8 6.4 1.0 N2 E:DG18 4.9 4.5 1.0 CA A:PRO145 5.0 3.8 1.0 O A:PRO145 5.0 4.2 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ O:F101 b:5.7 occ:1.00 FAF O:DLU101 0.0 5.7 1.0 CAT O:DLU101 1.3 6.0 1.0 CAJ O:DLU101 2.3 3.7 1.0 CAH O:DLU101 2.3 3.9 1.0 N1 N:DG18 2.9 4.6 1.0 C6 N:DG18 3.0 2.9 1.0 C2 N:DG18 3.2 2.6 1.0 CG I:GLN146 3.3 5.1 1.0 C5 N:DG18 3.3 3.1 1.0 O I:HOH411 3.4 7.9 1.0 O6 N:DG18 3.5 5.3 1.0 NE2 I:GLN146 3.5 5.5 1.0 CD I:GLN146 3.5 6.3 1.0 CAU O:DLU101 3.5 4.3 1.0 CAI O:DLU101 3.5 4.5 1.0 C4 N:DG18 3.6 2.8 1.0 N3 N:DG18 3.6 2.0 1.0 N I:GLN146 3.8 5.5 1.0 CA I:GLN146 3.8 3.1 1.0 N2 N:DG18 3.9 3.9 1.0 CAV O:DLU101 4.0 5.8 1.0 CB I:GLN146 4.1 5.8 1.0 C I:PRO145 4.2 3.6 1.0 N7 N:DG18 4.2 3.7 1.0 OE1 I:GLN146 4.2 8.9 1.0 N3 O:DC20 4.2 5.4 1.0 CB I:PRO145 4.4 5.9 1.0 O I:PRO145 4.5 4.3 1.0 FAG O:DLU101 4.5 8.9 1.0 N4 O:DC20 4.5 4.8 1.0 N9 N:DG18 4.5 2.4 1.0 C4 O:DC20 4.6 4.7 1.0 C8 N:DG18 4.8 4.0 1.0 C2 O:DC20 4.9 5.6 1.0 CA I:PRO145 4.9 3.8 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 Intasome Core Bound with Dtg


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 Bound with Dtg within 5.0Å range: probe atom residue distance (Å) B Occ O:F101 b:8.9 occ:1.00 FAG O:DLU101 0.0 8.9 1.0 CAU O:DLU101 1.2 4.3 1.0 CAJ O:DLU101 2.3 3.7 1.0 CAV O:DLU101 2.3 5.8 1.0 NAP O:DLU101 2.7 8.2 1.0 CAN O:DLU101 2.7 5.8 1.0 CG I:GLU152 3.1 3.3 1.0 OE1 I:GLU152 3.2 8.9 1.0 C2' O:DC20 3.2 6.7 1.0 CD I:GLU152 3.3 5.2 1.0 CB I:GLU152 3.3 2.9 1.0 OAD O:DLU101 3.5 9.7 1.0 CAT O:DLU101 3.5 6.0 1.0 CAI O:DLU101 3.5 4.5 1.0 N1 O:DC20 3.7 8.1 1.0 C2 O:DC20 3.7 5.6 1.0 CB I:PRO145 3.8 5.9 1.0 CAR O:DLU101 3.8 6.5 1.0 C1' O:DC20 3.9 5.8 1.0 O2 O:DC20 3.9 5.0 1.0 CAH O:DLU101 4.0 3.9 1.0 C6 O:DC20 4.2 6.2 1.0 OE2 I:GLU152 4.2 6.2 1.0 N3 O:DC20 4.3 5.4 1.0 CAZ O:DLU101 4.3 6.7 1.0 CAX O:DLU101 4.5 6.9 1.0 FAF O:DLU101 4.5 5.7 1.0 CA I:GLU152 4.5 2.6 1.0 C3' O:DC20 4.6 8.7 1.0 C5 O:DC20 4.6 4.9 1.0 C4 O:DC20 4.7 4.7 1.0 OAB O:DLU101 4.7 14.7 1.0 CG I:PRO145 4.7 7.2 1.0 MG I:MG302 4.8 6.3 1.0 N2 N:DG18 4.9 3.9 1.0 CA I:PRO145 5.0 3.8 1.0

M.Li, X.Chen, Z.Li, Y.Cui, A.Engelman, R.Craigie. Hiv-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies By Cryo-Em and Reveal the Role of the Integrase C-Terminal Tail in Hiv-1 Integration Viruses 2024.
ISSN: ESSN 1999-4915