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Yttrium 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:

Fluorine (F) 4 atoms

Yttrium Binding Sites:

The binding sites of Yttrium 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 Yttrium atom.
In total 9 binding sites of Yttrium where determined in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Yttrium binding site 1 out of 9 in 6prf

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Yttrium binding site 1 out of 9 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 Yttrium with other atoms in the Y 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
A:Y101

b:18.6
occ:0.20
 Y A:Y1103 1.1 22.2 0.2
Y A:Y1102 1.5 15.3 0.2
OE1 A:GLU58 2.1 39.4 1.0
O A:HOH257 2.4 19.9 0.3
O A:HOH207 2.4 12.9 0.3
O A:HOH271 2.5 21.3 0.2
O A:HOH278 2.6 19.4 0.3
OD1 A:ASP60 2.6 33.1 1.0
OD2 A:ASP60 3.2 33.4 1.0
CG A:ASP60 3.2 37.0 1.0
CD A:GLU58 3.2 32.3 1.0
O A:HOH247 3.8 20.8 0.3
OE2 A:GLU58 4.1 49.1 1.0
CG A:GLU58 4.1 19.5 1.0
CB A:ASP60 4.7 28.6 1.0
OG1 A:THR74 4.8 27.0 1.0
CG2 A:THR74 5.0 19.7 1.0

Yttrium binding site 2 out of 9 in 6prf

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Yttrium binding site 2 out of 9 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 Yttrium with other atoms in the Y 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
A:Y102

b:15.3
occ:0.20
 O A:HOH257 1.0 19.9 0.3
Y A:Y1101 1.5 18.6 0.2
O A:HOH207 1.8 12.9 0.3
O A:HOH271 2.3 21.3 0.2
O A:HOH278 2.4 19.4 0.3
OD2 A:ASP60 2.5 33.4 1.0
O A:HOH247 2.5 20.8 0.3
Y A:Y1103 2.6 22.2 0.2
OD1 A:ASP60 2.7 33.1 1.0
OE1 A:GLU58 2.8 39.4 1.0
CG A:ASP60 2.9 37.0 1.0
CD A:GLU58 3.9 32.3 1.0
CG A:GLU58 4.4 19.5 1.0
CB A:ASP60 4.4 28.6 1.0
O A:HOH295 4.5 32.1 1.0
CD A:LYS43 4.7 25.5 0.5
CG A:LYS43 4.7 35.9 0.5
CG A:LYS43 4.8 26.8 0.5
CB A:LYS43 4.9 30.2 0.5
OE2 A:GLU58 4.9 49.1 1.0

Yttrium binding site 3 out of 9 in 6prf

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Yttrium binding site 3 out of 9 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 Yttrium with other atoms in the Y 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
A:Y103

b:22.2
occ:0.20
 Y A:Y1101 1.1 18.6 0.2
OE1 A:GLU58 2.2 39.4 1.0
Y A:Y1102 2.6 15.3 0.2
OD1 A:ASP60 2.9 33.1 1.0
O A:HOH278 3.1 19.4 0.3
O A:HOH271 3.1 21.3 0.2
O A:HOH207 3.1 12.9 0.3
CD A:GLU58 3.2 32.3 1.0
O A:HOH257 3.4 19.9 0.3
CG A:ASP60 3.7 37.0 1.0
OE2 A:GLU58 3.8 49.1 1.0
OD2 A:ASP60 3.9 33.4 1.0
OG1 A:THR74 4.3 27.0 1.0
CG A:GLU58 4.3 19.5 1.0
O A:HOH281 4.5 39.2 1.0
CG2 A:THR74 4.6 19.7 1.0
O A:HOH247 4.7 20.8 0.3

Yttrium binding site 4 out of 9 in 6prf

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Yttrium binding site 4 out of 9 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 Yttrium with other atoms in the Y 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
A:Y104

b:28.6
occ:0.35
 O A:HOH287 1.4 20.7 0.2
C A:GLY78 3.3 15.6 1.0
CG A:GLU34 3.3 27.7 1.0
N A:ASP35 3.5 21.1 1.0
O A:HOH251 3.5 41.0 1.0
N A:PRO79 3.6 17.7 1.0
CA A:GLY78 3.6 15.8 1.0
O A:GLY78 3.6 16.0 1.0
CA A:GLU34 3.9 14.3 1.0
CA A:PRO79 3.9 17.7 1.0
CD A:PRO79 4.0 19.4 1.0
N A:GLY78 4.0 13.7 1.0
CB A:GLU34 4.2 17.9 1.0
OE2 A:GLU34 4.2 40.5 1.0
C A:GLU34 4.3 15.6 1.0
CB A:PRO79 4.3 22.0 1.0
CD A:GLU34 4.3 34.7 1.0
OD1 A:ASP35 4.3 39.0 1.0
CG1 A:VAL77 4.4 13.6 0.5
CA A:ASP35 4.5 25.4 1.0
CG1 A:VAL77 4.6 15.0 0.5
O A:HOH228 4.7 35.1 1.0
CG A:PRO79 4.8 19.8 1.0
C A:VAL77 4.8 13.1 1.0
O A:PHE33 4.9 12.5 0.7
O A:PHE33 5.0 13.2 0.3
CG A:ASP35 5.0 39.6 1.0

Yttrium binding site 5 out of 9 in 6prf

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Yttrium binding site 5 out of 9 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 Yttrium with other atoms in the Y binding site number 5 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:Y102

b:74.1
occ:0.20
 Y B:Y1105 2.1 21.2 0.2
OE2 B:GLU58 2.6 35.2 1.0
O B:HOH279 2.9 24.2 0.5
Y B:Y1103 3.1 20.3 0.2
NZ B:LYS45 3.6 34.1 0.5
CD B:GLU58 3.6 30.3 1.0
O B:HOH224 4.1 18.5 0.2
OE1 B:GLU58 4.1 42.9 1.0
CE B:LYS45 4.5 28.2 0.5
Y B:Y1104 4.5 17.2 0.2
NZ B:LYS45 4.7 32.8 0.5
CG B:GLU58 4.8 19.4 1.0
OD1 B:ASP60 4.8 33.5 1.0
OG1 B:THR74 4.9 28.4 1.0
CG2 B:THR74 4.9 19.3 1.0
CE B:LYS45 5.0 34.8 0.5

Yttrium binding site 6 out of 9 in 6prf

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Yttrium binding site 6 out of 9 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 Yttrium with other atoms in the Y binding site number 6 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:Y103

b:20.3
occ:0.25
 Y B:Y1105 1.1 21.2 0.2
Y B:Y1104 1.5 17.2 0.2
OE2 B:GLU58 2.2 35.2 1.0
O B:HOH224 2.5 18.5 0.2
O B:HOH214 2.5 21.9 0.2
OD1 B:ASP60 2.6 33.5 1.0
CD B:GLU58 2.8 30.3 1.0
Y B:Y1102 3.1 74.1 0.2
OD2 B:ASP60 3.1 33.4 1.0
OE1 B:GLU58 3.1 42.9 1.0
CG B:ASP60 3.2 38.3 1.0
O B:HOH238 3.9 26.2 0.5
CG B:GLU58 4.1 19.4 1.0
CB B:ASP60 4.6 28.1 1.0
NZ B:LYS45 4.8 34.1 0.5
Y B:Y1106 4.8 27.0 0.3
OG1 B:THR74 4.8 28.4 1.0
O B:HOH294 4.9 38.5 0.5
O B:HOH215 5.0 29.0 0.5

Yttrium binding site 7 out of 9 in 6prf

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Yttrium binding site 7 out of 9 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 Yttrium with other atoms in the Y binding site number 7 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:Y104

b:17.2
occ:0.25
 O B:HOH214 1.3 21.9 0.2
Y B:Y1103 1.5 20.3 0.2
O B:HOH224 2.2 18.5 0.2
OD2 B:ASP60 2.4 33.4 1.0
Y B:Y1105 2.6 21.2 0.2
O B:HOH238 2.7 26.2 0.5
OD1 B:ASP60 2.7 33.5 1.0
CG B:ASP60 2.9 38.3 1.0
OE1 B:GLU58 3.0 42.9 1.0
OE2 B:GLU58 3.0 35.2 1.0
CD B:GLU58 3.2 30.3 1.0
CG B:GLU58 4.3 19.4 1.0
O B:HOH215 4.4 29.0 0.5
CB B:ASP60 4.4 28.1 1.0
Y B:Y1102 4.5 74.1 0.2
O B:HOH291 4.5 33.4 1.0
Y B:Y1106 4.6 27.0 0.3
CG B:LYS43 4.7 36.0 1.0
O B:HOH294 4.8 38.5 0.5
CD B:LYS43 5.0 41.5 1.0

Yttrium binding site 8 out of 9 in 6prf

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Yttrium binding site 8 out of 9 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 Yttrium with other atoms in the Y binding site number 8 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:Y105

b:21.2
occ:0.20
 Y B:Y1103 1.1 20.3 0.2
OE2 B:GLU58 2.0 35.2 1.0
Y B:Y1102 2.1 74.1 0.2
Y B:Y1104 2.6 17.2 0.2
OD1 B:ASP60 2.9 33.5 1.0
CD B:GLU58 3.0 30.3 1.0
O B:HOH224 3.1 18.5 0.2
O B:HOH214 3.5 21.9 0.2
OE1 B:GLU58 3.5 42.9 1.0
CG B:ASP60 3.7 38.3 1.0
OD2 B:ASP60 3.9 33.4 1.0
CG B:GLU58 4.2 19.4 1.0
OG1 B:THR74 4.3 28.4 1.0
O B:HOH279 4.4 24.2 0.5
NZ B:LYS45 4.6 34.1 0.5
CG2 B:THR74 4.6 19.3 1.0
O B:HOH238 4.9 26.2 0.5

Yttrium binding site 9 out of 9 in 6prf

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Yttrium binding site 9 out of 9 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 Yttrium with other atoms in the Y binding site number 9 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:Y106

b:27.0
occ:0.30
 O B:HOH215 1.4 29.0 0.5
O B:HOH294 1.5 38.5 0.5
O B:HOH224 3.1 18.5 0.2
NZ B:LYS43 3.9 41.8 1.0
CE B:LYS43 4.4 43.7 1.0
Y B:Y1104 4.6 17.2 0.2
CD B:LYS43 4.6 41.5 1.0
Y B:Y1103 4.8 20.3 0.2

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: Sat Oct 12 20:49:46 2024

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