Fluorine in PDB 6vdk: Cryoem Structure of Hiv-1 Conserved Intasome Core

The structure of Cryoem Structure of Hiv-1 Conserved Intasome Core also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Cryoem Structure of Hiv-1 Conserved Intasome Core (pdb code 6vdk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cryoem Structure of Hiv-1 Conserved Intasome Core, PDB code: 6vdk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:0.7 occ:1.00 FAF A:DLU303 0.0 0.7 1.0 CAT A:DLU303 1.4 0.7 1.0 CAJ A:DLU303 2.4 0.7 1.0 CAH A:DLU303 2.4 0.7 1.0 OE1 A:GLN146 3.0 0.9 1.0 CD A:GLN146 3.3 0.9 1.0 C6 G:DG18 3.5 0.5 1.0 N1 G:DG18 3.5 0.5 1.0 CG A:GLN146 3.6 0.9 1.0 CAU A:DLU303 3.6 0.7 1.0 CAI A:DLU303 3.6 0.7 1.0 C5 G:DG18 3.8 0.5 1.0 O6 G:DG18 3.9 0.5 1.0 C2 G:DG18 3.9 0.5 1.0 C4 G:DG18 4.1 0.5 1.0 NE2 A:GLN146 4.1 0.9 1.0 CAV A:DLU303 4.1 0.7 1.0 CA A:GLN146 4.2 0.9 1.0 N3 G:DG18 4.2 0.5 1.0 O A:PRO145 4.3 99.8 1.0 N4 H:DC20 4.4 0.8 1.0 N A:GLN146 4.4 0.9 1.0 C A:PRO145 4.4 99.8 1.0 CB A:GLN146 4.4 0.9 1.0 N3 H:DC20 4.4 0.8 1.0 N7 G:DG18 4.5 0.5 1.0 N2 G:DG18 4.5 0.5 1.0 C4 H:DC20 4.7 0.8 1.0 FAG A:DLU303 4.8 0.7 1.0 N9 G:DG18 4.9 0.5 1.0 CB A:PRO145 5.0 99.8 1.0

Fluorine binding site 2 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:0.7 occ:1.00 FAG A:DLU303 0.0 0.7 1.0 CAU A:DLU303 1.4 0.7 1.0 CAJ A:DLU303 2.4 0.7 1.0 CAV A:DLU303 2.4 0.7 1.0 NAP A:DLU303 2.8 0.7 1.0 CAN A:DLU303 2.8 0.7 1.0 CG A:GLU152 3.2 0.5 1.0 CB A:GLU152 3.4 0.5 1.0 O2 H:DC20 3.4 0.8 1.0 CAT A:DLU303 3.6 0.7 1.0 CAI A:DLU303 3.6 0.7 1.0 C2 H:DC20 3.7 0.8 1.0 OAD A:DLU303 3.7 0.7 1.0 CD A:GLU152 3.9 0.5 1.0 CB A:PRO145 3.9 99.8 1.0 O A:PRO145 3.9 99.8 1.0 C2' H:DC20 3.9 0.8 1.0 CAR A:DLU303 3.9 0.7 1.0 N1 H:DC20 4.1 0.8 1.0 CAH A:DLU303 4.1 0.7 1.0 OE1 A:GLU152 4.1 0.5 1.0 C1' H:DC20 4.2 0.8 1.0 N3 H:DC20 4.3 0.8 1.0 N2 G:DG18 4.5 0.5 1.0 CAZ A:DLU303 4.5 0.7 1.0 OE2 A:GLU152 4.6 0.5 1.0 OAB A:DLU303 4.7 0.7 1.0 CAX A:DLU303 4.7 0.7 1.0 C A:PRO145 4.7 99.8 1.0 CA A:GLY149 4.7 0.5 1.0 FAF A:DLU303 4.8 0.7 1.0 CA A:GLU152 4.9 0.5 1.0 CA A:PRO145 4.9 99.8 1.0 C6 H:DC20 4.9 0.8 1.0

Fluorine binding site 3 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ C:F303 b:0.8 occ:1.00 FAF C:DLU303 0.0 0.8 1.0 CAT C:DLU303 1.4 0.8 1.0 CAH C:DLU303 2.4 0.8 1.0 CAJ C:DLU303 2.4 0.8 1.0 NE2 C:GLN146 3.0 0.5 1.0 CD C:GLN146 3.1 0.5 1.0 N1 E:DG18 3.3 0.1 1.0 C6 E:DG18 3.4 0.1 1.0 OE1 C:GLN146 3.5 0.5 1.0 CAU C:DLU303 3.6 0.8 1.0 CAI C:DLU303 3.6 0.8 1.0 C2 E:DG18 3.7 0.1 1.0 CG C:GLN146 3.7 0.5 1.0 O6 E:DG18 3.7 0.1 1.0 C5 E:DG18 3.8 0.1 1.0 N3 F:DC20 3.9 0.1 1.0 C4 E:DG18 4.0 0.1 1.0 N3 E:DG18 4.1 0.1 1.0 CAV C:DLU303 4.1 0.8 1.0 N2 E:DG18 4.2 0.1 1.0 O C:PRO145 4.3 0.2 1.0 CA C:GLN146 4.3 0.5 1.0 N4 F:DC20 4.4 0.1 1.0 C C:PRO145 4.5 0.2 1.0 C4 F:DC20 4.5 0.1 1.0 N C:GLN146 4.5 0.5 1.0 N7 E:DG18 4.6 0.1 1.0 CB C:GLN146 4.6 0.5 1.0 C2 F:DC20 4.7 0.1 1.0 O2 F:DC20 4.7 0.1 1.0 FAG C:DLU303 4.8 0.8 1.0 CB C:PRO145 4.9 0.2 1.0 N9 E:DG18 4.9 0.1 1.0

Fluorine binding site 4 out of 4 in the Cryoem Structure of Hiv-1 Conserved Intasome Core


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryoem Structure of Hiv-1 Conserved Intasome Core within 5.0Å range: probe atom residue distance (Å) B Occ C:F303 b:0.8 occ:1.00 FAG C:DLU303 0.0 0.8 1.0 CAU C:DLU303 1.4 0.8 1.0 CAJ C:DLU303 2.4 0.8 1.0 CAV C:DLU303 2.4 0.8 1.0 NAP C:DLU303 2.8 0.8 1.0 CAN C:DLU303 2.8 0.8 1.0 CB C:GLU152 3.1 0.1 1.0 CG C:GLU152 3.2 0.1 1.0 O2 F:DC20 3.2 0.1 1.0 C2' F:DC20 3.2 0.1 1.0 CD C:GLU152 3.4 0.1 1.0 OE1 C:GLU152 3.5 0.1 1.0 OAD C:DLU303 3.6 0.8 1.0 C2 F:DC20 3.6 0.1 1.0 CAT C:DLU303 3.6 0.8 1.0 CAI C:DLU303 3.6 0.8 1.0 CAR C:DLU303 3.9 0.8 1.0 C1' F:DC20 3.9 0.1 1.0 N1 F:DC20 3.9 0.1 1.0 CAH C:DLU303 4.1 0.8 1.0 CB C:PRO145 4.1 0.2 1.0 OE2 C:GLU152 4.2 0.1 1.0 O C:PRO145 4.3 0.2 1.0 N3 F:DC20 4.4 0.1 1.0 CAZ C:DLU303 4.4 0.8 1.0 OAB C:DLU303 4.5 0.8 1.0 CA C:GLU152 4.5 0.1 1.0 CAX C:DLU303 4.6 0.8 1.0 C3' F:DC20 4.6 0.1 1.0 FAF C:DLU303 4.8 0.8 1.0 C6 F:DC20 4.8 0.1 1.0 N2 E:DG18 4.9 0.1 1.0 O3' F:DC20 5.0 0.1 1.0

M.Li, X.Chen, H.Wang, K.Jurado, A.Engelman, R.Craigie. A Peptide Derived From Ledgf Stimulates Hiv-1 Dna Integration and Facilitates Intasome Structural Studies J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638