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Fluorine in PDB 6prf: Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A

Enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A

All present enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf was solved by D.W.Kneller, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.55 / 1.21
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.565, 60.565, 85.139, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 19

Other elements in 6prf:

The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A also contains other interesting chemical elements:

Yttrium (Y) 9 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A (pdb code 6prf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6prf

Go back to Fluorine Binding Sites List in 6prf
Fluorine binding site 1 out of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:22.1
occ:0.50
 F1 B:7OA101 0.0 22.1 0.5
C33 B:7OA101 1.4 14.8 0.5
O B:HOH287 1.4 33.6 0.5
O B:HOH202 2.3 34.3 1.0
C35 B:7OA101 2.3 18.0 0.5
C06 B:7OA101 2.4 14.2 0.5
C15 B:7OA101 3.1 12.8 0.5
C11 B:7OA101 3.2 14.2 0.5
CG2 B:VAL82 3.5 24.3 1.0
NH2 B:ARG8 3.5 27.9 0.5
NH1 B:ARG8 3.6 43.0 0.5
C34 B:7OA101 3.6 14.6 0.5
C07 B:7OA101 3.6 13.0 0.5
O B:HOH278 3.7 45.2 1.0
O A:HOH234 3.8 14.9 0.5
O A:HOH255 3.8 20.1 1.0
C59 B:7OA101 4.0 12.9 0.5
C08 B:7OA101 4.1 15.2 0.5
C12 B:7OA101 4.2 12.0 0.5
C13 B:7OA101 4.3 12.2 0.5
CB B:VAL82 4.3 19.2 1.0
CZ B:ARG8 4.5 35.7 0.5
O2 B:7OA101 4.5 12.7 0.5
CZ B:ARG8 4.5 38.4 0.5
NE B:ARG8 4.5 29.7 0.5
O23 B:7OA101 4.6 12.8 0.5
F2 B:7OA101 4.7 22.1 0.5
O A:GLY27 4.7 12.1 1.0
NH2 B:ARG8 4.8 32.2 0.5
CG1 B:VAL82 4.8 26.1 1.0
C49 B:7OA101 4.8 12.2 0.5
CD1 B:LEU23 4.9 15.5 0.5
C32 B:7OA101 4.9 11.5 0.5
O A:GLY48 4.9 22.6 1.0
C21 B:7OA101 4.9 10.5 0.5

Fluorine binding site 2 out of 4 in 6prf

Go back to Fluorine Binding Sites List in 6prf
Fluorine binding site 2 out of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:21.9
occ:0.50
 F1 B:7OA101 0.0 21.9 0.5
C33 B:7OA101 1.4 15.4 0.5
O A:HOH239 1.4 35.3 0.5
C06 B:7OA101 2.3 14.8 0.5
O A:HOH208 2.4 34.4 1.0
C35 B:7OA101 2.4 16.6 0.5
C15 B:7OA101 3.1 12.8 0.5
C11 B:7OA101 3.2 14.6 0.5
NH2 A:ARG8 3.6 33.7 0.5
CG2 A:VAL82 3.6 24.7 1.0
C34 B:7OA101 3.6 15.2 0.5
C07 B:7OA101 3.6 12.9 0.5
O A:HOH280 3.6 30.6 0.5
O B:HOH228 3.7 14.8 0.5
O A:HOH305 3.8 45.4 1.0
O B:HOH249 3.8 19.1 1.0
C59 B:7OA101 4.0 12.2 0.5
C08 B:7OA101 4.1 15.6 0.5
NH1 A:ARG8 4.1 30.8 0.5
C12 B:7OA101 4.2 11.8 0.5
C13 B:7OA101 4.2 11.9 0.5
O B:HOH297 4.3 39.4 1.0
CB A:VAL82 4.3 18.5 1.0
O2 B:7OA101 4.5 13.3 0.5
CZ A:ARG8 4.5 37.8 0.5
NE A:ARG8 4.6 34.7 0.5
O23 B:7OA101 4.6 12.3 0.5
O B:GLY27 4.7 11.7 1.0
F2 B:7OA101 4.7 23.9 0.5
CG1 A:VAL82 4.8 27.2 1.0
C49 B:7OA101 4.8 12.5 0.5
C32 B:7OA101 4.9 11.7 0.5
C21 B:7OA101 4.9 10.4 0.5
CD1 A:LEU23 4.9 13.3 0.5
O B:GLY48 4.9 22.7 0.5
CD2 A:LEU23 4.9 14.8 0.5
N20 B:7OA101 5.0 11.9 0.5

Fluorine binding site 3 out of 4 in 6prf

Go back to Fluorine Binding Sites List in 6prf
Fluorine binding site 3 out of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:22.1
occ:0.50
 F2 B:7OA101 0.0 22.1 0.5
C34 B:7OA101 1.4 14.6 0.5
C08 B:7OA101 2.3 15.2 0.5
C35 B:7OA101 2.3 18.0 0.5
C A:GLY49 2.9 19.7 1.0
N A:ILE50 3.0 19.4 0.5
N A:ILE50 3.0 19.0 0.5
CG B:PRO81 3.2 31.4 1.0
CA A:ILE50 3.2 22.4 0.5
CD B:PRO81 3.2 23.6 1.0
O A:GLY49 3.3 25.0 1.0
C14 B:7OA101 3.4 12.1 0.5
CA A:GLY49 3.5 23.1 1.0
CG2 A:ILE50 3.5 24.7 0.5
C33 B:7OA101 3.6 14.8 0.5
C07 B:7OA101 3.6 13.0 0.5
CA A:ILE50 3.6 18.7 0.5
CB B:PRO81 3.7 28.8 1.0
C15 B:7OA101 3.9 12.8 0.5
CB A:ILE50 3.9 25.0 0.5
CG1 A:ILE50 4.0 16.0 0.5
C06 B:7OA101 4.1 14.2 0.5
CB A:ILE50 4.2 16.9 0.5
C13 B:7OA101 4.2 12.2 0.5
N B:PRO81 4.3 18.9 1.0
OG1 B:THR80 4.3 15.8 1.0
N A:GLY49 4.4 20.4 1.0
C A:ILE50 4.5 22.1 0.5
N B:VAL82 4.6 14.7 1.0
CA B:PRO81 4.6 21.7 1.0
O A:GLY48 4.6 22.6 1.0
C12 B:7OA101 4.6 12.0 0.5
F1 B:7OA101 4.7 22.1 0.5
O A:HOH204 4.7 30.9 0.5
O22 B:7OA101 4.8 11.3 0.5
O B:HOH211 4.8 14.7 1.0
C A:GLY48 4.8 19.1 1.0
O10 B:7OA101 4.9 11.7 0.5
C32 B:7OA101 4.9 11.5 0.5
CG2 B:VAL82 4.9 24.3 1.0
O9 B:7OA101 4.9 10.5 0.5
CB B:VAL82 4.9 19.2 1.0
O A:HOH242 5.0 31.4 0.5

Fluorine binding site 4 out of 4 in 6prf

Go back to Fluorine Binding Sites List in 6prf
Fluorine binding site 4 out of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F101

b:23.9
occ:0.50
 F2 B:7OA101 0.0 23.9 0.5
C34 B:7OA101 1.3 15.2 0.5
C35 B:7OA101 2.3 16.6 0.5
C08 B:7OA101 2.3 15.6 0.5
C B:GLY49 3.0 19.5 1.0
N B:ILE50 3.0 19.1 0.5
CA B:ILE50 3.1 23.5 0.5
N B:ILE50 3.1 18.2 0.5
CD A:PRO81 3.2 23.3 1.0
CG A:PRO81 3.3 30.4 1.0
O B:GLY49 3.3 24.9 1.0
C14 B:7OA101 3.4 13.1 0.5
CA B:GLY49 3.5 22.9 1.0
CA B:ILE50 3.5 17.3 0.5
C33 B:7OA101 3.6 15.4 0.5
C07 B:7OA101 3.6 12.9 0.5
CB A:PRO81 3.6 27.3 1.0
CG2 B:ILE50 3.7 26.9 0.5
C15 B:7OA101 3.8 12.8 0.5
CB B:ILE50 4.0 27.6 0.5
CG1 B:ILE50 4.1 16.1 0.5
C06 B:7OA101 4.1 14.8 0.5
CB B:ILE50 4.1 17.6 0.5
C13 B:7OA101 4.2 11.9 0.5
C B:ILE50 4.2 15.7 0.5
N A:PRO81 4.3 18.0 1.0
OG1 A:THR80 4.3 16.0 1.0
N B:GLY49 4.4 20.5 1.0
N A:VAL82 4.5 15.2 1.0
O A:HOH305 4.5 45.4 1.0
O B:ILE50 4.6 25.1 0.5
CA A:PRO81 4.6 21.6 1.0
C12 B:7OA101 4.6 11.8 0.5
O B:GLY48 4.6 22.7 0.5
F1 B:7OA101 4.7 21.9 0.5
O22 B:7OA101 4.8 11.2 0.5
O B:GLY48 4.8 20.9 0.5
O B:HOH211 4.8 14.7 1.0
C32 B:7OA101 4.8 11.7 0.5
C B:ILE50 4.9 18.6 0.5
C B:GLY48 4.9 20.1 0.5
O10 B:7OA101 4.9 11.6 0.5
CB A:VAL82 4.9 18.5 1.0
O9 B:7OA101 4.9 10.7 0.5
CG2 A:VAL82 5.0 24.7 1.0
C A:PRO81 5.0 15.4 1.0

Reference:

D.W.Kneller, J.Agniswamy, A.K.Ghosh, I.T.Weber. Potent Antiviral Hiv-1 Protease Inhibitor Combats Highly Drug Resistant Mutant PR20. Biochem.Biophys.Res.Commun. V. 519 61 2019.
ISSN: ESSN 1090-2104
PubMed: 31474336
DOI: 10.1016/J.BBRC.2019.08.126
Page generated: Fri Aug 2 00:28:20 2024

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