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Fluorine in PDB 5mma: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ379 (Compound 5'G)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ379 (Compound 5'G)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ379 (Compound 5'G):
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 XZ379 (Compound 5'G), PDB code: 5mma was solved by D.P.Maskell, V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.36 / 2.55
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.570, 159.570, 124.140, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.7

Other elements in 5mma:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ379 (Compound 5'G) 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 XZ379 (Compound 5'G) (pdb code 5mma). 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 XZ379 (Compound 5'G), PDB code: 5mma:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5mma

Go back to Fluorine Binding Sites List in 5mma
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 XZ379 (Compound 5'G)


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 XZ379 (Compound 5'G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F417

b:55.6
occ:1.00
 FAG A:VHT417 0.0 55.6 1.0
CAW A:VHT417 1.3 48.4 1.0
CAM A:VHT417 2.3 39.2 1.0
CAX A:VHT417 2.4 45.2 1.0
NAQ A:VHT417 2.7 45.8 1.0
CAO A:VHT417 2.8 40.3 1.0
OE1 A:GLU221 3.1 49.3 1.0
C2' D:DC16 3.1 48.8 1.0
CD A:GLU221 3.2 48.1 1.0
OAD A:VHT417 3.2 57.6 1.0
CG A:GLU221 3.3 45.6 1.0
CB A:GLU221 3.4 47.0 1.0
CAV A:VHT417 3.6 53.0 1.0
CAK A:VHT417 3.6 39.7 1.0
CB A:PRO214 3.7 57.4 1.0
N1 D:DC16 3.7 61.9 1.0
C6 D:DC16 3.9 58.3 1.0
OE2 A:GLU221 3.9 50.7 1.0
CAU A:VHT417 3.9 52.2 1.0
C1' D:DC16 4.0 48.3 1.0
CAJ A:VHT417 4.1 45.4 1.0
C2 D:DC16 4.1 55.0 1.0
CBA A:VHT417 4.2 61.6 1.0
C3' D:DC16 4.2 54.7 1.0
MG A:MG403 4.3 50.8 1.0
CG A:PRO214 4.3 60.7 1.0
C5 D:DC16 4.3 53.4 1.0
CAZ A:VHT417 4.5 56.8 1.0
CA A:GLU221 4.6 53.8 1.0
O2 D:DC16 4.6 54.9 1.0
N3 D:DC16 4.6 59.9 1.0
C4 D:DC16 4.7 54.5 1.0
FAF A:VHT417 4.7 62.1 1.0
O A:PRO214 4.7 59.1 1.0
O3' D:DC16 4.8 64.3 1.0
OAC A:VHT417 4.8 52.7 1.0
CA A:PRO214 4.9 47.7 1.0
C A:PRO214 5.0 54.1 1.0

Fluorine binding site 2 out of 2 in 5mma

Go back to Fluorine Binding Sites List in 5mma
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 XZ379 (Compound 5'G)


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 XZ379 (Compound 5'G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F417

b:62.1
occ:1.00
 FAF A:VHT417 0.0 62.1 1.0
CAV A:VHT417 1.3 53.0 1.0
CAJ A:VHT417 2.4 45.4 1.0
CAM A:VHT417 2.4 39.2 1.0
C6 C:DG4 3.1 56.4 1.0
N1 C:DG4 3.2 56.2 1.0
O6 C:DG4 3.3 57.4 1.0
CG A:GLN215 3.3 57.8 0.5
CG A:GLN215 3.4 57.4 0.5
N4 D:DC16 3.6 53.1 1.0
C5 C:DG4 3.6 58.5 1.0
CAW A:VHT417 3.6 48.4 1.0
CAK A:VHT417 3.6 39.7 1.0
CD A:GLN215 3.8 55.7 0.5
C2 C:DG4 3.8 55.8 1.0
C4 D:DC16 3.9 54.5 1.0
CA A:GLN215 3.9 53.9 0.5
N3 D:DC16 3.9 59.9 1.0
CA A:GLN215 3.9 54.0 0.5
N A:GLN215 3.9 50.0 1.0
OE1 A:GLN215 3.9 35.6 0.5
O C:HOH215 4.0 67.0 1.0
C4 C:DG4 4.1 58.1 1.0
CB A:GLN215 4.1 55.6 0.5
CAX A:VHT417 4.1 45.2 1.0
CB A:GLN215 4.2 55.6 0.5
N3 C:DG4 4.2 51.8 1.0
N7 C:DG4 4.4 55.1 1.0
C A:PRO214 4.4 54.1 1.0
N2 C:DG4 4.5 59.2 1.0
NE2 A:GLN215 4.5 56.0 0.5
CD A:GLN215 4.6 60.4 0.5
O A:PRO214 4.7 59.1 1.0
FAG A:VHT417 4.7 55.6 1.0
C2 D:DC16 4.7 55.0 1.0
C5 D:DC16 4.8 53.4 1.0
CG A:PRO214 4.8 60.7 1.0
NE2 A:GLN215 4.8 69.8 0.5
CB A:PRO214 5.0 57.4 1.0
O3 A:GOL413 5.0 92.7 1.0
N9 C:DG4 5.0 60.8 1.0

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 05:16:09 2025

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