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Fluorine in PDB 6dil: Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir

Protein crystallography data

The structure of Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir, PDB code: 6dil was solved by A.E.Wong-Sam, Y.-F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.77 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.604, 86.403, 46.156, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.4

Other elements in 6dil:

The structure of Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir (pdb code 6dil). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir, PDB code: 6dil:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 1 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:32.0
occ:0.70
 F40 B:TPV201 0.0 32.0 0.7
C39 B:TPV201 1.3 17.0 0.7
C16 B:TPV201 1.4 15.7 0.3
F42 B:TPV201 2.1 25.0 0.7
C17 B:TPV201 2.2 14.5 0.3
F41 B:TPV201 2.2 25.6 0.7
C36 B:TPV201 2.3 18.5 0.7
C15 B:TPV201 2.4 14.6 0.3
O A:HOH601 2.6 12.8 0.3
C35 B:TPV201 2.8 18.6 0.7
CZ B:ARG8 3.3 15.5 1.0
NE B:ARG8 3.3 13.8 1.0
C18 B:TPV201 3.4 14.9 0.3
CD2 B:LEU23 3.5 14.1 1.0
C37 B:TPV201 3.5 20.4 0.7
NH1 B:ARG8 3.6 19.7 1.0
C14 B:TPV201 3.6 12.1 0.3
CD B:ARG8 3.7 14.4 1.0
NH2 B:ARG8 3.8 14.9 1.0
C19 B:TPV201 3.9 13.5 0.3
CG2 B:VAL82 4.1 14.8 0.3
O A:GLY27 4.1 12.9 1.0
N34 B:TPV201 4.2 15.7 0.7
CG1 B:VAL82 4.2 21.4 0.7
CD1 B:LEU23 4.4 15.5 1.0
O A:HOH615 4.4 17.1 0.7
CG1 B:VAL82 4.5 13.1 0.3
CG B:LEU23 4.5 10.5 1.0
O B:HOH350 4.7 29.9 1.0
CG B:ARG8 4.7 11.3 1.0
OD1 A:ASP29 4.7 12.4 1.0
C38 B:TPV201 4.7 21.1 0.7
C13 B:TPV201 4.7 10.9 0.3
CB B:VAL82 4.8 17.1 0.7
C12 B:TPV201 4.9 13.7 0.3
CB B:VAL82 4.9 14.4 0.3
C33 B:TPV201 4.9 22.1 0.7

Fluorine binding site 2 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 2 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:27.9
occ:0.30
 F40 B:TPV201 0.0 27.9 0.3
C39 B:TPV201 1.3 17.5 0.3
C18 B:TPV201 1.5 15.2 0.7
F41 B:TPV201 2.2 57.7 0.3
F42 B:TPV201 2.2 49.9 0.3
C36 B:TPV201 2.2 20.6 0.3
C19 B:TPV201 2.4 14.1 0.7
C17 B:TPV201 2.6 16.2 0.7
C35 B:TPV201 2.9 23.4 0.3
O B:HOH301 2.9 25.6 1.0
NE A:ARG8 3.0 18.3 1.0
CZ A:ARG8 3.0 19.2 1.0
NH2 A:ARG8 3.3 22.9 1.0
C37 B:TPV201 3.3 21.8 0.3
CD A:ARG8 3.3 18.8 1.0
NH1 A:ARG8 3.6 18.4 1.0
C14 B:TPV201 3.7 14.0 0.7
C16 B:TPV201 3.8 16.1 0.7
CD2 A:LEU23 3.8 13.2 1.0
C3 B:GOL203 4.0 21.7 0.7
N34 B:TPV201 4.2 23.3 0.3
C15 B:TPV201 4.3 14.9 0.7
O B:GLY27 4.4 17.0 1.0
CG A:ARG8 4.4 14.7 1.0
O A:HOH645 4.4 24.7 0.5
C38 B:TPV201 4.5 22.0 0.3
O3 B:GOL203 4.5 21.3 0.7
CG2 A:VAL82 4.6 20.1 0.4
OD1 B:ASP29 4.6 16.2 1.0
CG1 A:VAL82 4.7 20.0 0.6
CD1 A:LEU23 4.7 14.0 1.0
C33 B:TPV201 4.8 22.1 0.3
CG A:LEU23 4.8 10.4 1.0
C13 B:TPV201 4.8 13.9 0.7
CG2 A:VAL82 4.9 25.4 0.6
CG1 A:VAL82 4.9 23.0 0.4
O B:HOH322 4.9 17.7 1.0

Fluorine binding site 3 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 3 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:25.6
occ:0.70
 F41 B:TPV201 0.0 25.6 0.7
C17 B:TPV201 0.5 14.5 0.3
C39 B:TPV201 1.3 17.0 0.7
C18 B:TPV201 1.7 14.9 0.3
C16 B:TPV201 1.7 15.7 0.3
F42 B:TPV201 2.1 25.0 0.7
F40 B:TPV201 2.2 32.0 0.7
C36 B:TPV201 2.2 18.5 0.7
C37 B:TPV201 2.6 20.4 0.7
C19 B:TPV201 2.8 13.5 0.3
C15 B:TPV201 2.8 14.6 0.3
C14 B:TPV201 3.3 12.1 0.3
NH1 B:ARG8 3.4 19.7 1.0
O B:HOH379 3.5 47.3 1.0
CZ B:ARG8 3.5 15.5 1.0
NH2 B:ARG8 3.5 14.9 1.0
C35 B:TPV201 3.5 18.6 0.7
CG1 B:VAL82 3.7 13.1 0.3
O B:HOH368 3.8 58.3 1.0
C38 B:TPV201 4.0 21.1 0.7
O B:HOH330 4.1 36.5 1.0
CG2 B:VAL82 4.2 14.8 0.3
NE B:ARG8 4.3 13.8 1.0
CG1 B:VAL82 4.3 21.4 0.7
CB B:PRO81 4.3 22.0 1.0
CB B:VAL82 4.4 17.1 0.7
O A:HOH601 4.5 12.8 0.3
CB B:VAL82 4.6 14.4 0.3
N34 B:TPV201 4.7 15.7 0.7
C13 B:TPV201 4.7 10.9 0.3
CG B:PRO81 4.8 26.1 1.0
C33 B:TPV201 4.8 22.1 0.7
O B:HOH350 4.9 29.9 1.0
CD B:ARG8 5.0 14.4 1.0

Fluorine binding site 4 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 4 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:57.7
occ:0.30
 F41 B:TPV201 0.0 57.7 0.3
C17 B:TPV201 0.7 16.2 0.7
C39 B:TPV201 1.3 17.5 0.3
C18 B:TPV201 1.4 15.2 0.7
C16 B:TPV201 2.1 16.1 0.7
F40 B:TPV201 2.2 27.9 0.3
F42 B:TPV201 2.2 49.9 0.3
C36 B:TPV201 2.2 20.6 0.3
C37 B:TPV201 2.6 21.8 0.3
C19 B:TPV201 2.7 14.1 0.7
C15 B:TPV201 3.1 14.9 0.7
C14 B:TPV201 3.4 14.0 0.7
NH2 A:ARG8 3.4 22.9 1.0
CG2 A:VAL82 3.5 20.1 0.4
C35 B:TPV201 3.5 23.4 0.3
CH3 A:ACT504 3.6 0.0 1.0
CZ A:ARG8 3.6 19.2 1.0
NH1 A:ARG8 3.8 18.4 1.0
OXT A:ACT504 3.8 0.9 1.0
C38 B:TPV201 4.0 22.0 0.3
C A:ACT504 4.1 0.5 1.0
CG1 A:VAL82 4.1 20.0 0.6
C3 B:GOL203 4.2 21.7 0.7
CB A:VAL82 4.3 18.0 0.6
CB A:VAL82 4.3 19.1 0.4
NE A:ARG8 4.3 18.3 1.0
N34 B:TPV201 4.6 23.3 0.3
CG2 A:VAL82 4.7 25.4 0.6
C1 B:GOL203 4.7 22.7 0.7
C13 B:TPV201 4.7 13.9 0.7
O A:HOH645 4.8 24.7 0.5
O B:HOH301 4.8 25.6 1.0
CG1 A:VAL82 4.8 23.0 0.4
C33 B:TPV201 4.8 22.1 0.3
CD A:ARG8 4.9 18.8 1.0

Fluorine binding site 5 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 5 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:25.0
occ:0.70
 F42 B:TPV201 0.0 25.0 0.7
C15 B:TPV201 0.7 14.6 0.3
C16 B:TPV201 0.8 15.7 0.3
C39 B:TPV201 1.4 17.0 0.7
C14 B:TPV201 1.6 12.1 0.3
C17 B:TPV201 1.7 14.5 0.3
F40 B:TPV201 2.1 32.0 0.7
F41 B:TPV201 2.1 25.6 0.7
C19 B:TPV201 2.2 13.5 0.3
C36 B:TPV201 2.2 18.5 0.7
C18 B:TPV201 2.2 14.9 0.3
C13 B:TPV201 2.9 10.9 0.3
C37 B:TPV201 3.0 20.4 0.7
C35 B:TPV201 3.0 18.6 0.7
C12 B:TPV201 3.5 13.7 0.3
CG2 B:VAL82 3.5 14.8 0.3
C22 B:TPV201 3.5 15.7 0.7
CG1 B:VAL82 3.5 21.4 0.7
CD2 B:LEU23 3.9 14.1 1.0
C21 B:TPV201 3.9 15.7 0.7
O A:HOH601 3.9 12.8 0.3
C38 B:TPV201 4.2 21.1 0.7
CG B:PRO81 4.2 26.1 1.0
N34 B:TPV201 4.2 15.7 0.7
CB B:VAL82 4.4 17.1 0.7
CG1 B:VAL82 4.4 13.1 0.3
CB B:PRO81 4.5 22.0 1.0
O A:GLY27 4.5 12.9 1.0
CB B:VAL82 4.6 14.4 0.3
C33 B:TPV201 4.6 22.1 0.7
CZ B:ARG8 4.9 15.5 1.0

Fluorine binding site 6 out of 6 in 6dil

Go back to Fluorine Binding Sites List in 6dil
Fluorine binding site 6 out of 6 in the Hiv-1 Protease with Single Mutation L76V 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 Hiv-1 Protease with Single Mutation L76V in Complex with Tipranavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:49.9
occ:0.30
 F42 B:TPV201 0.0 49.9 0.3
C19 B:TPV201 0.7 14.1 0.7
C18 B:TPV201 1.0 15.2 0.7
C39 B:TPV201 1.3 17.5 0.3
C14 B:TPV201 1.7 14.0 0.7
C17 B:TPV201 2.0 16.2 0.7
F40 B:TPV201 2.2 27.9 0.3
C36 B:TPV201 2.2 20.6 0.3
F41 B:TPV201 2.2 57.7 0.3
C15 B:TPV201 2.4 14.9 0.7
C16 B:TPV201 2.5 16.1 0.7
C35 B:TPV201 2.6 23.4 0.3
C13 B:TPV201 2.9 13.9 0.7
CG1 A:VAL82 3.2 20.0 0.6
C37 B:TPV201 3.3 21.8 0.3
C22 B:TPV201 3.4 18.9 0.3
CD2 A:LEU23 3.7 13.2 1.0
C12 B:TPV201 3.8 12.1 0.7
N34 B:TPV201 3.9 23.3 0.3
C21 B:TPV201 4.0 14.0 0.3
CG2 A:VAL82 4.0 20.1 0.4
O B:HOH301 4.0 25.6 1.0
CB A:VAL82 4.1 18.0 0.6
CB A:VAL82 4.1 19.1 0.4
C3 B:GOL203 4.1 21.7 0.7
CG1 A:VAL82 4.3 23.0 0.4
O B:GLY27 4.4 17.0 1.0
C38 B:TPV201 4.4 22.0 0.3
CG2 A:VAL82 4.5 25.4 0.6
O3 B:GOL203 4.6 21.3 0.7
C33 B:TPV201 4.6 22.1 0.3
CD1 A:ILE84 4.8 14.6 0.4
CZ A:ARG8 4.9 19.2 1.0

Reference:

A.Wong-Sam, Y.F.Wang, Y.Zhang, A.K.Ghosh, R.W.Harrison, I.T.Weber. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of Hiv-1 Protease. Acs Omega V. 3 12132 2018.
ISSN: ESSN 2470-1343
PubMed: 30288468
DOI: 10.1021/ACSOMEGA.8B01683
Page generated: Thu Aug 1 18:55:06 2024

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