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Fluorine in PDB 7adv: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V):
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V), PDB code: 7adv was solved by V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.16 / 2.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 158.61, 158.61, 122.95, 90, 90, 90
R / Rfree (%) 19.6 / 21.9

Other elements in 7adv:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) (pdb code 7adv). 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 the Insti XZ447 (Compound 6V), PDB code: 7adv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7adv

Go back to Fluorine Binding Sites List in 7adv
Fluorine binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)


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 the Insti XZ447 (Compound 6V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:59.9
occ:1.00
 F8 A:R7N404 0.0 59.9 1.0
C7 A:R7N404 1.3 48.1 1.0
C6 A:R7N404 2.3 40.9 1.0
C2 A:R7N404 2.4 41.5 1.0
C1 A:R7N404 2.8 41.9 1.0
N11 A:R7N404 2.8 55.1 1.0
OE1 A:GLU221 3.0 55.5 1.0
C2' D:DC16 3.2 47.7 1.0
CD A:GLU221 3.3 52.4 1.0
O21 A:R7N404 3.3 61.7 1.0
CB A:GLU221 3.4 48.9 1.0
CG A:GLU221 3.4 52.6 1.0
C5 A:R7N404 3.6 50.9 1.0
N1 D:DC16 3.6 45.5 1.0
C3 A:R7N404 3.6 43.4 1.0
CB A:PRO214 3.7 53.1 1.0
C6 D:DC16 3.7 55.6 1.0
C1' D:DC16 3.9 45.3 1.0
OE2 A:GLU221 4.0 54.7 1.0
C2 D:DC16 4.0 55.8 1.0
C12 A:R7N404 4.1 62.0 1.0
C4 A:R7N404 4.1 46.6 1.0
C5 D:DC16 4.1 46.8 1.0
CG A:PRO214 4.3 58.5 1.0
C3' D:DC16 4.3 60.1 1.0
C16 A:R7N404 4.3 62.3 1.0
MG A:MG402 4.3 54.6 1.0
N3 D:DC16 4.5 54.2 1.0
C4 D:DC16 4.5 50.8 1.0
CA A:GLU221 4.6 51.7 1.0
O2 D:DC16 4.6 57.1 1.0
C15 A:R7N404 4.6 65.0 1.0
O A:PRO214 4.7 57.3 1.0
F10 A:R7N404 4.7 61.2 1.0
CA A:PRO214 4.9 54.2 1.0
O13 A:R7N404 4.9 55.5 1.0
O3' D:DC16 4.9 65.6 1.0
C A:PRO214 4.9 55.4 1.0

Fluorine binding site 2 out of 2 in 7adv

Go back to Fluorine Binding Sites List in 7adv
Fluorine binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)


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 the Insti XZ447 (Compound 6V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:61.2
occ:1.00
 F10 A:R7N404 0.0 61.2 1.0
C5 A:R7N404 1.4 50.9 1.0
C6 A:R7N404 2.4 40.9 1.0
C4 A:R7N404 2.4 46.6 1.0
C6 C:DG4 3.2 53.4 1.0
CG A:GLN215 3.2 63.3 0.4
CG A:GLN215 3.2 62.7 0.6
O6 C:DG4 3.3 59.4 1.0
N1 C:DG4 3.3 54.6 1.0
CD A:GLN215 3.5 54.5 0.4
N4 D:DC16 3.5 44.9 1.0
C7 A:R7N404 3.6 48.1 1.0
C3 A:R7N404 3.6 43.4 1.0
C5 C:DG4 3.7 53.5 1.0
OE1 A:GLN215 3.7 46.7 0.4
C4 D:DC16 3.9 50.8 1.0
CA A:GLN215 3.9 56.9 0.4
CA A:GLN215 3.9 49.4 0.6
N A:GLN215 3.9 49.9 1.0
C2 C:DG4 4.0 54.5 1.0
N3 D:DC16 4.1 54.2 1.0
NE2 A:GLN215 4.1 67.0 0.4
CB A:GLN215 4.1 54.1 0.4
CB A:GLN215 4.1 49.6 0.6
C2 A:R7N404 4.1 41.5 1.0
C4 C:DG4 4.2 57.1 1.0
CD A:GLN215 4.3 61.9 0.6
NE2 A:GLN215 4.4 73.7 0.6
N7 C:DG4 4.4 53.7 1.0
N3 C:DG4 4.4 50.8 1.0
C A:PRO214 4.5 55.4 1.0
N2 C:DG4 4.7 51.4 1.0
CG A:PRO214 4.7 58.5 1.0
F8 A:R7N404 4.7 59.9 1.0
C5 D:DC16 4.7 46.8 1.0
O A:PRO214 4.8 57.3 1.0
CB A:PRO214 4.9 53.1 1.0
O D:HOH217 5.0 73.9 1.0
C2 D:DC16 5.0 55.8 1.0

Reference:

S.J.Smith, X.Z.Zhao, D.O.Passos, V.E.Pye, P.Cherepanov, D.Lyumkis, T.R.Burke Jr., S.H.Hughes. Hiv-1 Integrase Inhibitors with Modifications That Affect Their Potencies Against Drug Resistant Integrase Mutants. Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
PubMed: 33686850
DOI: 10.1021/ACSINFECDIS.0C00819
Page generated: Tue Jul 15 18:32:48 2025

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