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Yttrium in PDB 4ye3: Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A

Enzymatic activity of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A

All present enzymatic activity of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A, PDB code: 4ye3 was solved by J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.35
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.349, 60.349, 85.775, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 20

Other elements in 4ye3:

The structure of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A (pdb code 4ye3). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 4 binding sites of Yttrium where determined in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A, PDB code: 4ye3:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in 4ye3

Go back to Yttrium Binding Sites List in 4ye3
Yttrium binding site 1 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y101

b:23.3
occ:0.40
Y A:Y1102 1.3 21.6 0.2
CL A:CL103 1.7 31.3 0.5
O A:HOH217 2.2 23.0 0.5
OD2 A:ASP35 2.3 26.7 1.0
O A:HOH201 2.4 18.5 0.3
CL A:CL104 2.6 20.3 0.3
OE2 A:GLU34 2.7 27.6 0.5
OD1 A:ASP35 2.7 35.3 1.0
CG A:ASP35 2.8 25.9 1.0
OE1 A:GLU34 2.8 34.1 0.5
CD A:GLU34 3.2 26.9 0.5
OE1 A:GLU34 3.8 26.2 0.5
CD A:GLU34 3.8 28.0 0.5
CG A:GLU34 3.9 20.6 0.5
CB A:ASP35 4.3 21.8 1.0
OE2 A:GLU34 4.4 31.2 0.5
O A:HOH273 4.6 32.7 0.5
CG A:GLU34 4.9 23.6 0.5
O A:HOH269 5.0 23.6 1.0

Yttrium binding site 2 out of 4 in 4ye3

Go back to Yttrium Binding Sites List in 4ye3
Yttrium binding site 2 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y102

b:21.6
occ:0.20
Y A:Y1101 1.3 23.3 0.4
CL A:CL104 1.3 20.3 0.3
O A:HOH201 1.9 18.5 0.3
OD2 A:ASP35 2.6 26.7 1.0
CL A:CL103 2.9 31.3 0.5
OE2 A:GLU34 2.9 27.6 0.5
O A:HOH217 3.3 23.0 0.5
OE1 A:GLU34 3.5 34.1 0.5
CG A:ASP35 3.5 25.9 1.0
CD A:GLU34 3.8 26.9 0.5
OD1 A:ASP35 3.8 35.3 1.0
CG A:GLU34 4.3 20.6 0.5
O A:HOH269 4.5 23.6 1.0
OE1 A:GLU34 4.6 26.2 0.5
CD A:GLU34 4.7 28.0 0.5
CB A:ASP35 4.9 21.8 1.0

Yttrium binding site 3 out of 4 in 4ye3

Go back to Yttrium Binding Sites List in 4ye3
Yttrium binding site 3 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y202

b:23.8
occ:0.40
Y B:Y1203 1.2 12.0 0.1
OE2 B:GLU58 2.2 27.5 1.0
O B:HOH332 2.2 30.4 0.6
CL B:CL204 2.3 45.7 0.4
CL B:CL205 2.6 26.6 0.5
OD1 B:ASP60 2.8 31.5 1.0
OD2 B:ASP60 3.2 40.4 1.0
CD B:GLU58 3.4 27.6 1.0
CG B:ASP60 3.4 28.2 1.0
OE1 B:GLU58 4.1 36.4 1.0
OG1 B:THR74 4.3 26.0 1.0
CG B:GLU58 4.4 17.8 1.0
CG2 B:THR74 4.7 20.7 1.0
CB B:ASP60 4.8 25.0 1.0

Yttrium binding site 4 out of 4 in 4ye3

Go back to Yttrium Binding Sites List in 4ye3
Yttrium binding site 4 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20 with Inhibitor Grl-4410A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y203

b:12.0
occ:0.10
Y B:Y1202 1.2 23.8 0.4
CL B:CL205 1.4 26.6 0.5
OE2 B:GLU58 2.3 27.5 1.0
OD2 B:ASP60 2.5 40.4 1.0
OD1 B:ASP60 2.6 31.5 1.0
CG B:ASP60 2.9 28.2 1.0
O B:HOH332 3.3 30.4 0.6
CD B:GLU58 3.3 27.6 1.0
CL B:CL204 3.5 45.7 0.4
O B:HOH334 4.0 42.2 1.0
OE1 B:GLU58 4.0 36.4 1.0
CG B:GLU58 4.2 17.8 1.0
CB B:ASP60 4.4 25.0 1.0
OG1 B:THR74 4.9 26.0 1.0

Reference:

J.Agniswamy, J.M.Louis, C.H.Shen, S.Yashchuk, A.K.Ghosh, I.T.Weber. Substituted Bis-Thf Protease Inhibitors with Improved Potency Against Highly Resistant Mature Hiv-1 Protease PR20. J.Med.Chem. V. 58 5088 2015.
ISSN: ISSN 0022-2623
PubMed: 26010498
DOI: 10.1021/ACS.JMEDCHEM.5B00474
Page generated: Wed Dec 16 02:41:14 2020

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