Fluorine in PDB 3s3m: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3m was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.15 / 2.49
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.140, 160.140, 123.430, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.2

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) (pdb code 3s3m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range: probe atom residue distance (Å) B Occ A:F398 b:43.0 occ:1.00 FAF A:DLU398 0.0 43.0 1.0 CAT A:DLU398 1.3 39.3 1.0 CAJ A:DLU398 2.3 38.0 1.0 CAH A:DLU398 2.4 36.7 1.0 C6 C:DG4 2.9 40.0 1.0 N1 C:DG4 3.1 38.8 1.0 O6 C:DG4 3.1 40.7 1.0 CG A:GLN215 3.3 39.4 0.5 C5 C:DG4 3.5 39.2 1.0 CG A:GLN215 3.5 38.1 0.5 CAU A:DLU398 3.6 39.7 1.0 N4 D:DC16 3.7 39.7 1.0 CAI A:DLU398 3.7 36.6 1.0 C2 C:DG4 3.8 37.3 1.0 CD A:GLN215 3.8 38.9 0.5 N A:GLN215 3.8 38.4 1.0 OE1 A:GLN215 3.8 35.5 0.5 CA A:GLN215 3.8 38.7 0.5 CA A:GLN215 3.8 38.4 0.5 C4 D:DC16 4.0 40.3 1.0 C4 C:DG4 4.0 38.9 1.0 N3 D:DC16 4.1 42.1 1.0 CB A:GLN215 4.1 38.7 0.5 CAV A:DLU398 4.1 37.8 1.0 O C:HOH253 4.2 47.3 1.0 CB A:GLN215 4.2 38.3 0.5 N3 C:DG4 4.2 37.0 1.0 N7 C:DG4 4.2 40.7 1.0 C A:PRO214 4.5 38.5 1.0 N2 C:DG4 4.5 35.0 1.0 FAG A:DLU398 4.7 42.8 1.0 CD A:GLN215 4.7 35.7 0.5 NE2 A:GLN215 4.7 41.3 0.5 OE1 A:GLN215 4.9 39.2 0.5 O A:PRO214 4.9 38.0 1.0 C5 D:DC16 4.9 38.8 1.0 C2 D:DC16 5.0 42.9 1.0 N9 C:DG4 5.0 41.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range: probe atom residue distance (Å) B Occ A:F398 b:42.8 occ:1.00 FAG A:DLU398 0.0 42.8 1.0 CAU A:DLU398 1.3 39.7 1.0 CAJ A:DLU398 2.3 38.0 1.0 CAV A:DLU398 2.4 37.8 1.0 CAN A:DLU398 2.9 36.1 1.0 NAP A:DLU398 2.9 37.6 1.0 C2' D:DC16 3.1 42.0 1.0 CB A:GLU221 3.2 37.6 1.0 CG A:GLU221 3.3 36.5 1.0 OE1 A:GLU221 3.4 40.5 1.0 N1 D:DC16 3.5 42.5 1.0 CD A:GLU221 3.5 39.7 1.0 CAT A:DLU398 3.6 39.3 1.0 CAI A:DLU398 3.7 36.6 1.0 C6 D:DC16 3.7 41.9 1.0 OAD A:DLU398 3.7 42.0 1.0 C2 D:DC16 3.8 42.9 1.0 C1' D:DC16 3.8 41.3 1.0 CB A:PRO214 3.8 39.5 1.0 CAH A:DLU398 4.1 36.7 1.0 CAR A:DLU398 4.1 40.6 1.0 O2 D:DC16 4.2 43.6 1.0 C5 D:DC16 4.2 38.8 1.0 N3 D:DC16 4.2 42.1 1.0 OE2 A:GLU221 4.3 40.4 1.0 C3' D:DC16 4.4 47.1 1.0 CG A:PRO214 4.4 39.2 1.0 C4 D:DC16 4.4 40.3 1.0 CA A:GLU221 4.4 37.5 1.0 FAF A:DLU398 4.7 43.0 1.0 MG A:MG397 4.7 39.6 1.0 CAZ A:DLU398 4.7 43.0 1.0 O A:PRO214 4.8 38.0 1.0 C A:PRO214 4.9 38.5 1.0 C A:GLU221 4.9 37.9 1.0 CAX A:DLU398 4.9 41.1 1.0 CA A:PRO214 4.9 39.1 1.0 OAB A:DLU398 4.9 40.4 1.0 N2 C:DG4 5.0 35.0 1.0 O4' D:DC16 5.0 42.6 1.0

S.Hare, S.J.Smith, M.Metifiot, A.Jaxa-Chamiec, Y.Pommier, S.H.Hughes, P.Cherepanov. Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Mol.Pharmacol. V. 80 565 2011.
ISSN: ISSN 0026-895X
PubMed: 21719464
DOI: 10.1124/MOL.111.073189