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Fluorine in PDB 6dif: Wild-Type Hiv-1 Protease in Complex with Tipranavir

Protein crystallography data

The structure of Wild-Type Hiv-1 Protease in Complex with Tipranavir, PDB code: 6dif 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) 25.00 / 1.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.300, 86.259, 46.005, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.7

Other elements in 6dif:

The structure of Wild-Type Hiv-1 Protease in Complex with Tipranavir also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 6dif

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

b:19.0
occ:0.70
 F40 B:TPV201 0.0 19.0 0.7
C16 B:TPV201 1.3 14.8 0.3
C39 B:TPV201 1.3 12.6 0.7
F42 B:TPV201 2.1 19.7 0.7
F41 B:TPV201 2.1 16.9 0.7
C17 B:TPV201 2.3 15.0 0.3
C36 B:TPV201 2.3 11.2 0.7
C15 B:TPV201 2.3 13.7 0.3
O A:HOH601 2.6 10.5 0.3
C35 B:TPV201 2.8 10.8 0.7
CZ B:ARG8 3.3 12.7 1.0
NE B:ARG8 3.3 11.4 1.0
CD2 B:LEU23 3.4 11.6 1.0
NH1 B:ARG8 3.5 16.7 1.0
C37 B:TPV201 3.5 12.5 0.7
C18 B:TPV201 3.5 15.0 0.3
C14 B:TPV201 3.6 12.7 0.3
CD B:ARG8 3.7 11.9 1.0
NH2 B:ARG8 3.8 12.9 1.0
CG2 B:VAL82 4.0 18.8 1.0
C19 B:TPV201 4.0 14.8 0.3
O A:GLY27 4.1 14.3 1.0
N34 B:TPV201 4.1 11.4 0.7
O A:HOH612 4.2 12.1 0.7
CG1 B:VAL82 4.2 20.9 1.0
CD1 B:LEU23 4.4 11.6 1.0
CG B:LEU23 4.5 7.7 1.0
OD1 A:ASP29 4.6 9.7 1.0
CG B:ARG8 4.7 9.8 1.0
C38 B:TPV201 4.7 13.3 0.7
CB B:VAL82 4.7 15.7 1.0
C13 B:TPV201 4.7 12.6 0.3
O B:HOH359 4.8 27.6 1.0
C12 B:TPV201 4.9 12.4 0.3
C33 B:TPV201 4.9 11.3 0.7
O A:HOH616 4.9 6.2 0.3

Fluorine binding site 2 out of 6 in 6dif

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

b:20.0
occ:0.30
 F40 B:TPV201 0.0 20.0 0.3
C39 B:TPV201 1.3 15.4 0.3
C18 B:TPV201 1.5 13.6 0.7
F41 B:TPV201 2.2 73.7 0.3
F42 B:TPV201 2.2 36.7 0.3
C19 B:TPV201 2.2 12.5 0.7
C36 B:TPV201 2.3 16.6 0.3
O B:HOH312 2.6 19.0 1.0
C35 B:TPV201 2.8 16.4 0.3
C17 B:TPV201 2.8 14.5 0.7
NE A:ARG8 3.2 13.9 1.0
CZ A:ARG8 3.3 15.7 1.0
CD A:ARG8 3.4 14.7 1.0
C37 B:TPV201 3.4 17.2 0.3
CD2 A:LEU23 3.5 12.4 1.0
NH2 A:ARG8 3.5 19.2 1.0
C14 B:TPV201 3.6 10.3 0.7
NH1 A:ARG8 3.9 17.2 1.0
C16 B:TPV201 4.0 12.2 0.7
N34 B:TPV201 4.0 13.8 0.3
O B:GLY27 4.1 15.6 1.0
C3 B:GOL203 4.2 13.1 0.7
C15 B:TPV201 4.2 10.8 0.7
CG A:ARG8 4.3 13.0 1.0
CG1 A:VAL82 4.4 13.2 0.5
OD1 B:ASP29 4.5 12.4 1.0
CD1 A:LEU23 4.5 13.4 1.0
C38 B:TPV201 4.5 15.4 0.3
CG A:LEU23 4.6 10.5 1.0
CG2 A:VAL82 4.6 17.8 0.5
C13 B:TPV201 4.6 11.3 0.7
O A:HOH679 4.7 21.0 0.5
O B:HOH324 4.7 12.5 1.0
C33 B:TPV201 4.7 14.4 0.3
O3 B:GOL203 4.8 14.6 0.7
C22 B:TPV201 4.8 14.4 0.3
CG1 A:VAL82 4.8 20.0 0.5
CG2 A:VAL82 4.8 16.6 0.5
CB A:VAL82 5.0 15.6 0.5
CB A:VAL82 5.0 15.1 0.5

Fluorine binding site 3 out of 6 in 6dif

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

b:16.9
occ:0.70
 F41 B:TPV201 0.0 16.9 0.7
C17 B:TPV201 0.7 15.0 0.3
C39 B:TPV201 1.3 12.6 0.7
C16 B:TPV201 1.5 14.8 0.3
C18 B:TPV201 2.0 15.0 0.3
F42 B:TPV201 2.1 19.7 0.7
F40 B:TPV201 2.1 19.0 0.7
C36 B:TPV201 2.3 11.2 0.7
C15 B:TPV201 2.7 13.7 0.3
C37 B:TPV201 2.8 12.5 0.7
C19 B:TPV201 3.0 14.8 0.3
CG1 B:VAL82 3.3 20.9 1.0
C14 B:TPV201 3.3 12.7 0.3
NH1 B:ARG8 3.3 16.7 1.0
CZ B:ARG8 3.5 12.7 1.0
C35 B:TPV201 3.6 10.8 0.7
O B:HOH355 3.6 37.4 1.0
NH2 B:ARG8 3.7 12.9 1.0
O B:HOH402 3.8 27.0 0.5
CG2 B:VAL82 3.9 18.8 1.0
CB B:VAL82 4.1 15.7 1.0
C38 B:TPV201 4.2 13.3 0.7
NE B:ARG8 4.3 11.4 1.0
O B:HOH363 4.3 35.9 1.0
CB B:PRO81 4.4 20.0 1.0
O A:HOH601 4.5 10.5 0.3
C13 B:TPV201 4.6 12.6 0.3
N34 B:TPV201 4.8 11.4 0.7
CG B:PRO81 4.8 20.0 1.0
O B:HOH359 4.8 27.6 1.0
CD B:ARG8 4.9 11.9 1.0
C B:PRO81 4.9 16.8 1.0
C33 B:TPV201 5.0 11.3 0.7
O B:PRO81 5.0 17.7 1.0

Fluorine binding site 4 out of 6 in 6dif

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

b:73.7
occ:0.30
 F41 B:TPV201 0.0 73.7 0.3
C17 B:TPV201 1.1 14.5 0.7
C18 B:TPV201 1.3 13.6 0.7
C39 B:TPV201 1.3 15.4 0.3
F40 B:TPV201 2.2 20.0 0.3
F42 B:TPV201 2.2 36.7 0.3
C36 B:TPV201 2.2 16.6 0.3
C16 B:TPV201 2.5 12.2 0.7
C37 B:TPV201 2.6 17.2 0.3
C19 B:TPV201 2.7 12.5 0.7
NH2 A:ARG8 3.0 19.2 1.0
CZ A:ARG8 3.3 15.7 1.0
C15 B:TPV201 3.4 10.8 0.7
CG2 A:VAL82 3.5 17.8 0.5
C14 B:TPV201 3.5 10.3 0.7
C35 B:TPV201 3.5 16.4 0.3
NH1 A:ARG8 3.6 17.2 1.0
O A:HOH648 3.6 29.3 0.5
NE A:ARG8 4.0 13.9 1.0
O A:HOH659 4.0 22.8 0.5
C38 B:TPV201 4.0 15.4 0.3
CG1 A:VAL82 4.1 13.2 0.5
CB A:VAL82 4.3 15.1 0.5
CB A:VAL82 4.3 15.6 0.5
C3 B:GOL203 4.4 13.1 0.7
O A:HOH679 4.5 21.0 0.5
CD A:ARG8 4.5 14.7 1.0
CG2 A:VAL82 4.5 16.6 0.5
O B:HOH312 4.5 19.0 1.0
C1 B:GOL203 4.6 15.5 0.7
N34 B:TPV201 4.7 13.8 0.3
CG1 A:VAL82 4.8 20.0 0.5
C13 B:TPV201 4.8 11.3 0.7
C33 B:TPV201 4.8 14.4 0.3

Fluorine binding site 5 out of 6 in 6dif

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

b:19.7
occ:0.70
 F42 B:TPV201 0.0 19.7 0.7
C15 B:TPV201 0.8 13.7 0.3
C16 B:TPV201 1.0 14.8 0.3
C39 B:TPV201 1.4 12.6 0.7
C14 B:TPV201 1.7 12.7 0.3
C17 B:TPV201 2.0 15.0 0.3
F41 B:TPV201 2.1 16.9 0.7
F40 B:TPV201 2.1 19.0 0.7
C36 B:TPV201 2.2 11.2 0.7
C19 B:TPV201 2.4 14.8 0.3
C18 B:TPV201 2.5 15.0 0.3
C13 B:TPV201 2.9 12.6 0.3
C35 B:TPV201 3.1 10.8 0.7
C37 B:TPV201 3.1 12.5 0.7
CG2 B:VAL82 3.3 18.8 1.0
C22 B:TPV201 3.5 10.8 0.7
C12 B:TPV201 3.5 12.4 0.3
C21 B:TPV201 3.8 12.5 0.7
CD2 B:LEU23 3.8 11.6 1.0
O A:HOH601 3.9 10.5 0.3
CG1 B:VAL82 4.1 20.9 1.0
CG B:PRO81 4.2 20.0 1.0
CB B:VAL82 4.3 15.7 1.0
N34 B:TPV201 4.3 11.4 0.7
C38 B:TPV201 4.4 13.3 0.7
O A:GLY27 4.5 14.3 1.0
CB B:PRO81 4.5 20.0 1.0
C33 B:TPV201 4.8 11.3 0.7
CZ B:ARG8 5.0 12.7 1.0
N B:VAL82 5.0 14.4 1.0

Fluorine binding site 6 out of 6 in 6dif

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

b:36.7
occ:0.30
 F42 B:TPV201 0.0 36.7 0.3
C19 B:TPV201 0.8 12.5 0.7
C18 B:TPV201 1.1 13.6 0.7
C39 B:TPV201 1.3 15.4 0.3
C14 B:TPV201 1.6 10.3 0.7
C17 B:TPV201 2.0 14.5 0.7
F40 B:TPV201 2.2 20.0 0.3
C36 B:TPV201 2.2 16.6 0.3
F41 B:TPV201 2.2 73.7 0.3
C15 B:TPV201 2.3 10.8 0.7
C16 B:TPV201 2.5 12.2 0.7
C35 B:TPV201 2.8 16.4 0.3
C13 B:TPV201 2.8 11.3 0.7
C22 B:TPV201 3.0 14.4 0.3
CG1 A:VAL82 3.1 13.2 0.5
C37 B:TPV201 3.3 17.2 0.3
C12 B:TPV201 3.8 9.8 0.7
C21 B:TPV201 3.8 11.8 0.3
CD2 A:LEU23 3.9 12.4 1.0
CG2 A:VAL82 3.9 17.8 0.5
CB A:VAL82 4.0 15.6 0.5
CB A:VAL82 4.0 15.1 0.5
N34 B:TPV201 4.1 13.8 0.3
O B:HOH312 4.1 19.0 1.0
C3 B:GOL203 4.3 13.1 0.7
CG1 A:VAL82 4.3 20.0 0.5
O B:GLY27 4.4 15.6 1.0
C38 B:TPV201 4.4 15.4 0.3
CG2 A:VAL82 4.5 16.6 0.5
C33 B:TPV201 4.7 14.4 0.3
CZ A:ARG8 4.9 15.7 1.0
NH2 A:ARG8 5.0 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 18:54:44 2024

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