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Fluorine in PDB 5no1: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G):
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 XZ407 (Compound 5G), PDB code: 5no1 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) 56.06 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 158.570, 158.570, 123.060, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 5no1:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ407 (Compound 5G) 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 XZ407 (Compound 5G) (pdb code 5no1). 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 XZ407 (Compound 5G), PDB code: 5no1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5no1

Go back to Fluorine Binding Sites List in 5no1
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 XZ407 (Compound 5G)


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 XZ407 (Compound 5G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:80.9
occ:1.00
 F8 A:XZ4403 0.0 80.9 1.0
C7 A:XZ4403 1.3 64.7 1.0
C6 A:XZ4403 2.3 58.8 1.0
C2 A:XZ4403 2.3 58.8 1.0
C1 A:XZ4403 2.7 62.8 1.0
N10 A:XZ4403 2.8 58.8 1.0
C2' D:DC16 3.1 65.2 1.0
OE1 A:GLU221 3.2 64.9 1.0
O19 A:XZ4403 3.3 79.8 1.0
CD A:GLU221 3.4 53.1 1.0
CB A:GLU221 3.4 52.3 1.0
CG A:GLU221 3.4 53.3 1.0
C5 A:XZ4403 3.5 71.9 1.0
C3 A:XZ4403 3.5 58.8 1.0
N1 D:DC16 3.7 68.7 1.0
CB A:PRO214 3.7 67.6 1.0
C6 D:DC16 3.8 72.2 1.0
C11 A:XZ4403 3.9 75.4 1.0
C1' D:DC16 3.9 64.5 1.0
C4 A:XZ4403 4.0 60.1 1.0
OE2 A:GLU221 4.1 78.8 1.0
C2 D:DC16 4.2 65.5 1.0
C14 A:XZ4403 4.2 83.4 1.0
C5 D:DC16 4.3 65.3 1.0
C3' D:DC16 4.3 69.8 1.0
MG A:MG401 4.4 58.8 1.0
CA A:GLU221 4.6 65.7 1.0
C13 A:XZ4403 4.6 82.0 1.0
CG A:PRO214 4.6 63.0 1.0
F9 A:XZ4403 4.6 83.6 1.0
O5' D:DA17 4.6 92.7 1.0
O2 D:DC16 4.6 80.3 1.0
N3 D:DC16 4.6 78.6 1.0
O12 A:XZ4403 4.7 66.8 1.0
C4 D:DC16 4.7 64.9 1.0
O3' D:DC16 4.9 75.8 1.0
O A:PRO214 4.9 70.2 1.0
C5' D:DA17 4.9 0.0 1.0
CA A:PRO214 5.0 54.1 1.0

Fluorine binding site 2 out of 2 in 5no1

Go back to Fluorine Binding Sites List in 5no1
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 XZ407 (Compound 5G)


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 XZ407 (Compound 5G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:83.6
occ:1.00
 F9 A:XZ4403 0.0 83.6 1.0
C5 A:XZ4403 1.3 71.9 1.0
C6 A:XZ4403 2.3 58.8 1.0
C4 A:XZ4403 2.3 60.1 1.0
N1 C:DG4 3.1 64.0 1.0
C6 C:DG4 3.1 59.7 1.0
O6 C:DG4 3.4 71.2 1.0
CG A:GLN215 3.4 67.4 0.5
N4 D:DC16 3.5 65.2 1.0
CG A:GLN215 3.5 65.5 0.5
C7 A:XZ4403 3.6 64.7 1.0
C3 A:XZ4403 3.6 58.8 1.0
C2 C:DG4 3.6 71.0 1.0
C5 C:DG4 3.7 60.0 1.0
C4 D:DC16 3.7 64.9 1.0
N3 D:DC16 3.7 78.6 1.0
N A:GLN215 3.8 60.2 1.0
OE1 A:GLN215 3.9 53.9 0.5
CA A:GLN215 3.9 61.8 0.5
CA A:GLN215 3.9 61.9 0.5
CD A:GLN215 3.9 66.3 0.5
C2 A:XZ4403 4.1 58.8 1.0
C4 C:DG4 4.1 67.7 1.0
O C:HOH212 4.1 71.3 1.0
N3 C:DG4 4.2 65.0 1.0
CB A:GLN215 4.2 59.0 0.5
CB A:GLN215 4.2 59.7 0.5
N2 C:DG4 4.3 64.8 1.0
C A:PRO214 4.4 70.0 1.0
N7 C:DG4 4.5 66.8 1.0
C5 D:DC16 4.5 65.3 1.0
C2 D:DC16 4.6 65.5 1.0
F8 A:XZ4403 4.6 80.9 1.0
CD A:GLN215 4.7 74.6 0.5
O A:PRO214 4.7 70.2 1.0
CB A:PRO214 4.7 67.6 1.0
NE2 A:GLN215 4.8 73.2 0.5
NE2 A:GLN215 4.9 62.2 0.5

Reference:

X.Z.Zhao, S.J.Smith, D.P.Maskell, M.Metifiot, V.E.Pye, K.Fesen, C.Marchand, Y.Pommier, P.Cherepanov, S.H.Hughes, T.R.Burke. Structure-Guided Optimization of Hiv Integrase Strand Transfer Inhibitors. J. Med. Chem. V. 60 7315 2017.
ISSN: ISSN 1520-4804
PubMed: 28737946
DOI: 10.1021/ACS.JMEDCHEM.7B00596
Page generated: Tue Jul 15 05:32:07 2025

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