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Fluorine in PDB 2o4l: Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir, PDB code: 2o4l was solved by A.A.Armstrong, S.Muzammil, A.Jakalian, P.R.Bonneau, V.Schmelmer, E.Freire, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.35 / 1.33
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.957, 86.411, 46.186, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.6

Other elements in 2o4l:

The structure of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir (pdb code 2o4l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir, PDB code: 2o4l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 1 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


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 Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:18.9
occ:0.70
F40 A:TPV403 0.0 18.9 0.7
C39 A:TPV403 1.3 16.8 0.7
C16 A:TPV403 1.8 10.5 0.3
F42 A:TPV403 2.1 18.6 0.7
F41 A:TPV403 2.2 18.5 0.7
C36 A:TPV403 2.4 15.5 0.7
C15 A:TPV403 2.4 11.9 0.3
O A:HOH589 2.6 7.3 0.3
C35 A:TPV403 2.8 13.5 0.7
C17 A:TPV403 3.0 10.4 0.3
NE B:ARG8 3.2 14.8 1.0
CZ B:ARG8 3.2 16.2 1.0
NH1 B:ARG8 3.4 17.9 1.0
CD B:ARG8 3.4 13.5 1.0
CD2 B:LEU23 3.4 11.9 1.0
C37 A:TPV403 3.6 15.0 0.7
C14 A:TPV403 3.8 10.5 0.3
NH2 B:ARG8 3.8 16.4 1.0
O A:GLY27 3.9 14.4 1.0
O A:HOH587 4.0 14.2 0.7
N34 A:TPV403 4.1 14.5 0.7
C18 A:TPV403 4.2 10.2 0.3
CD1 B:LEU23 4.3 13.1 1.0
CG2 B:VAL82 4.3 16.6 1.0
CG B:ARG8 4.4 11.7 1.0
O B:HOH437 4.4 23.0 1.0
CG B:LEU23 4.4 10.7 1.0
OD1 A:ASP29 4.5 11.9 1.0
C19 A:TPV403 4.5 11.0 0.3
C1 A:GOL405 4.5 7.5 0.3
CG1 B:VAL82 4.6 17.0 1.0
O A:HOH434 4.7 2.7 0.3
C38 A:TPV403 4.8 16.2 0.7
C22 A:TPV403 4.8 12.6 0.7
C13 A:TPV403 4.9 10.2 0.3
C21 A:TPV403 4.9 13.1 0.7
C33 A:TPV403 5.0 14.5 0.7

Fluorine binding site 2 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 2 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


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 Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:14.8
occ:0.30
F40 A:TPV403 0.0 14.8 0.3
C39 A:TPV403 1.3 14.0 0.3
C16 A:TPV403 1.9 12.6 0.7
F42 A:TPV403 2.1 15.9 0.3
F41 A:TPV403 2.2 16.1 0.3
C36 A:TPV403 2.3 13.8 0.3
O B:HOH420 2.5 10.6 0.7
C15 A:TPV403 2.5 11.5 0.7
C35 A:TPV403 2.7 13.0 0.3
NE A:ARG8 3.1 14.5 1.0
CD A:ARG8 3.1 13.7 1.0
C17 A:TPV403 3.1 12.2 0.7
CZ A:ARG8 3.3 15.8 1.0
CD2 A:LEU23 3.3 13.6 1.0
NH1 A:ARG8 3.5 17.9 1.0
C37 A:TPV403 3.6 13.1 0.3
C14 A:TPV403 3.9 11.9 0.7
CG A:ARG8 4.0 11.4 1.0
NH2 A:ARG8 4.0 14.3 1.0
N34 A:TPV403 4.0 12.8 0.3
O B:GLY27 4.1 14.4 1.0
CD1 A:LEU23 4.2 12.6 1.0
CG A:LEU23 4.3 11.0 1.0
C18 A:TPV403 4.3 12.7 0.7
CG1 A:VAL82 4.4 12.8 0.5
O A:HOH450 4.4 23.9 1.0
OD1 B:ASP29 4.4 11.6 1.0
O B:HOH408 4.5 11.8 1.0
C1 B:GOL404 4.5 12.2 0.7
C19 A:TPV403 4.6 9.7 0.7
CG2 A:VAL82 4.7 14.4 0.5
C38 A:TPV403 4.7 12.1 0.3
CB A:ARG8 4.7 11.0 1.0
C22 A:TPV403 4.8 8.7 0.3
C33 A:TPV403 4.9 11.9 0.3
C21 A:TPV403 4.9 9.6 0.3
CG1 A:VAL82 4.9 15.8 0.5
CG2 A:VAL82 4.9 14.5 0.5
C13 A:TPV403 5.0 12.5 0.7
CB A:VAL82 5.0 14.1 0.5
CB A:VAL82 5.0 13.8 0.5

Fluorine binding site 3 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 3 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:18.5
occ:0.70
F41 A:TPV403 0.0 18.5 0.7
C39 A:TPV403 1.3 16.8 0.7
C17 A:TPV403 1.5 10.4 0.3
C16 A:TPV403 1.6 10.5 0.3
F42 A:TPV403 2.1 18.6 0.7
F40 A:TPV403 2.2 18.9 0.7
C36 A:TPV403 2.4 15.5 0.7
NH1 B:ARG8 2.7 17.9 1.0
C37 A:TPV403 2.8 15.0 0.7
C18 A:TPV403 2.9 10.2 0.3
C15 A:TPV403 3.0 11.9 0.3
CZ B:ARG8 3.1 16.2 1.0
O B:HOH484 3.4 31.6 1.0
NH2 B:ARG8 3.4 16.4 1.0
CG1 B:VAL82 3.5 17.0 1.0
C35 A:TPV403 3.6 13.5 0.7
C19 A:TPV403 3.8 11.0 0.3
C14 A:TPV403 3.8 10.5 0.3
NE B:ARG8 3.9 14.8 1.0
O B:HOH465 4.1 20.8 1.0
O B:HOH437 4.1 23.0 1.0
CG2 B:VAL82 4.2 16.6 1.0
C38 A:TPV403 4.2 16.2 0.7
O B:HOH493 4.2 25.8 1.0
O A:HOH589 4.4 7.3 0.3
CD B:ARG8 4.5 13.5 1.0
CB B:VAL82 4.5 15.0 1.0
N34 A:TPV403 4.7 14.5 0.7
C1 A:GOL405 4.7 7.5 0.3
C3 A:GOL405 4.9 9.4 0.3
C33 A:TPV403 5.0 14.5 0.7

Fluorine binding site 4 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 4 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:16.1
occ:0.30
F41 A:TPV403 0.0 16.1 0.3
C39 A:TPV403 1.3 14.0 0.3
C16 A:TPV403 1.6 12.6 0.7
C17 A:TPV403 1.6 12.2 0.7
F42 A:TPV403 2.1 15.9 0.3
F40 A:TPV403 2.2 14.8 0.3
C36 A:TPV403 2.3 13.8 0.3
NH1 A:ARG8 2.5 17.9 1.0
C37 A:TPV403 2.8 13.1 0.3
CZ A:ARG8 2.9 15.8 1.0
C15 A:TPV403 3.0 11.5 0.7
C18 A:TPV403 3.0 12.7 0.7
NH2 A:ARG8 3.4 14.3 1.0
CG2 A:VAL82 3.4 14.4 0.5
NE A:ARG8 3.5 14.5 1.0
C35 A:TPV403 3.5 13.0 0.3
O A:HOH450 3.9 23.9 1.0
C14 A:TPV403 3.9 11.9 0.7
C19 A:TPV403 3.9 9.7 0.7
CD A:ARG8 4.0 13.7 1.0
O A:HOH478 4.1 28.5 1.0
CG1 A:VAL82 4.1 12.8 0.5
C38 A:TPV403 4.2 12.1 0.3
CB A:VAL82 4.3 13.8 0.5
CB A:VAL82 4.3 14.1 0.5
O B:HOH420 4.3 10.6 0.7
O A:HOH558 4.4 47.5 1.0
CG2 A:VAL82 4.5 14.5 0.5
N34 A:TPV403 4.6 12.8 0.3
C1 B:GOL404 4.7 12.2 0.7
CG1 A:VAL82 4.7 15.8 0.5
C33 A:TPV403 4.9 11.9 0.3
C3 B:GOL404 4.9 13.0 0.7

Fluorine binding site 5 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 5 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:18.6
occ:0.70
F42 A:TPV403 0.0 18.6 0.7
C16 A:TPV403 1.1 10.5 0.3
C15 A:TPV403 1.2 11.9 0.3
C39 A:TPV403 1.3 16.8 0.7
C17 A:TPV403 1.9 10.4 0.3
C14 A:TPV403 2.1 10.5 0.3
F40 A:TPV403 2.1 18.9 0.7
F41 A:TPV403 2.1 18.5 0.7
C36 A:TPV403 2.3 15.5 0.7
C18 A:TPV403 2.5 10.2 0.3
C19 A:TPV403 2.6 11.0 0.3
C35 A:TPV403 3.1 13.5 0.7
C37 A:TPV403 3.1 15.0 0.7
CG2 B:VAL82 3.2 16.6 1.0
C13 A:TPV403 3.3 10.2 0.3
C22 A:TPV403 3.4 12.6 0.7
C21 A:TPV403 3.7 13.1 0.7
CD2 B:LEU23 3.8 11.9 1.0
CG1 B:VAL82 4.0 17.0 1.0
O A:HOH589 4.0 7.3 0.3
CB B:VAL82 4.2 15.0 1.0
N34 A:TPV403 4.3 14.5 0.7
C38 A:TPV403 4.3 16.2 0.7
C12 A:TPV403 4.3 11.1 0.3
C1 A:GOL405 4.5 7.5 0.3
O A:GLY27 4.5 14.4 1.0
NH1 B:ARG8 4.7 17.9 1.0
CZ B:ARG8 4.7 16.2 1.0
C33 A:TPV403 4.8 14.5 0.7
CG B:PRO81 4.9 16.3 1.0
C20 A:TPV403 4.9 12.4 0.7
NH2 B:ARG8 5.0 16.4 1.0

Fluorine binding site 6 out of 6 in 2o4l

Go back to Fluorine Binding Sites List in 2o4l
Fluorine binding site 6 out of 6 in the Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hiv-1 Protease (Q7K, I50V) in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:15.9
occ:0.30
F42 A:TPV403 0.0 15.9 0.3
C16 A:TPV403 1.0 12.6 0.7
C15 A:TPV403 1.2 11.5 0.7
C39 A:TPV403 1.3 14.0 0.3
C17 A:TPV403 2.0 12.2 0.7
F41 A:TPV403 2.1 16.1 0.3
F40 A:TPV403 2.1 14.8 0.3
C14 A:TPV403 2.2 11.9 0.7
C36 A:TPV403 2.3 13.8 0.3
C18 A:TPV403 2.7 12.7 0.7
C19 A:TPV403 2.8 9.7 0.7
CG1 A:VAL82 2.9 12.8 0.5
C37 A:TPV403 3.1 13.1 0.3
C35 A:TPV403 3.2 13.0 0.3
C22 A:TPV403 3.4 8.7 0.3
C13 A:TPV403 3.4 12.5 0.7
CG2 A:VAL82 3.7 14.4 0.5
CD2 A:LEU23 3.7 13.6 1.0
CB A:VAL82 3.8 13.8 0.5
CB A:VAL82 3.8 14.1 0.5
C21 A:TPV403 3.9 9.6 0.3
O B:HOH420 4.0 10.6 0.7
CG1 A:VAL82 4.3 15.8 0.5
C38 A:TPV403 4.3 12.1 0.3
CG2 A:VAL82 4.3 14.5 0.5
C12 A:TPV403 4.3 13.1 0.7
N34 A:TPV403 4.4 12.8 0.3
O B:GLY27 4.5 14.4 1.0
C1 B:GOL404 4.5 12.2 0.7
NH1 A:ARG8 4.6 17.9 1.0
CZ A:ARG8 4.6 15.8 1.0
C33 A:TPV403 4.8 11.9 0.3
NE A:ARG8 4.9 14.5 1.0
NH2 A:ARG8 5.0 14.3 1.0

Reference:

S.Muzammil, A.A.Armstrong, L.W.Kang, A.Jakalian, P.R.Bonneau, V.Schmelmer, L.M.Amzel, E.Freire. Unique Thermodynamic Response of Tipranavir to Human Immunodeficiency Virus Type 1 Protease Drug Resistance Mutations. J.Virol. V. 81 5144 2007.
ISSN: ISSN 0022-538X
PubMed: 17360759
DOI: 10.1128/JVI.02706-06
Page generated: Sun Dec 13 11:38:15 2020

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