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Yttrium in PDB 4yhq: Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A

Enzymatic activity of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A

All present enzymatic activity of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A, PDB code: 4yhq 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 / 1.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.303, 60.303, 86.141, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 21

Other elements in 4yhq:

The structure of Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A (pdb code 4yhq). 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 Clinical Isolate PR20 with Grl-5010A, PDB code: 4yhq:
Jump to Yttrium binding site number: 1; 2; 3; 4;

Yttrium binding site 1 out of 4 in 4yhq

Go back to Yttrium Binding Sites List in 4yhq
Yttrium binding site 1 out of 4 in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A


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 Clinical Isolate PR20 with Grl-5010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y202

b:23.7
occ:0.30
 Y A:Y1203 1.3 14.7 0.1
CL A:CL204 1.5 13.9 0.2
OD2 A:ASP35 2.3 31.0 1.0
CL A:CL205 2.5 16.7 0.2
O A:HOH357 2.6 29.2 0.3
OD1 A:ASP35 2.7 35.2 1.0
CG A:ASP35 2.8 28.2 1.0
O A:HOH308 3.2 11.2 0.7
CD A:GLU34 3.4 33.7 1.0
OE1 A:GLU34 3.7 32.6 1.0
OE2 A:GLU34 3.7 43.9 1.0
CG A:GLU34 3.7 27.8 1.0
CB A:ASP35 4.3 22.9 1.0

Yttrium binding site 2 out of 4 in 4yhq

Go back to Yttrium Binding Sites List in 4yhq
Yttrium binding site 2 out of 4 in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A


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 Clinical Isolate PR20 with Grl-5010A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y203

b:14.7
occ:0.10
 CL A:CL205 1.2 16.7 0.2
Y A:Y1202 1.3 23.7 0.3
OD2 A:ASP35 2.6 31.0 1.0
CL A:CL204 2.7 13.9 0.2
CG A:ASP35 3.5 28.2 1.0
OD1 A:ASP35 3.8 35.2 1.0
O A:HOH357 3.8 29.2 0.3
OE2 A:GLU34 4.1 43.9 1.0
CD A:GLU34 4.1 33.7 1.0
CG A:GLU34 4.3 27.8 1.0
O A:HOH308 4.5 11.2 0.7
OE1 A:GLU34 4.7 32.6 1.0
O A:HOH377 4.8 23.7 1.0
CB A:ASP35 4.9 22.9 1.0

Yttrium binding site 3 out of 4 in 4yhq

Go back to Yttrium Binding Sites List in 4yhq
Yttrium binding site 3 out of 4 in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A


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 Clinical Isolate PR20 with Grl-5010A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y101

b:23.5
occ:0.30
 Y B:Y1102 1.4 14.8 0.1
O B:HOH210 1.5 17.7 0.7
OD1 B:ASP35 2.2 31.4 1.0
O B:HOH234 2.3 24.7 0.3
O B:HOH272 2.6 18.5 0.3
OD2 B:ASP35 2.7 36.8 1.0
CG B:ASP35 2.8 26.7 1.0
O B:HOH205 3.2 15.3 1.0
CD B:GLU34 3.5 34.2 1.0
OE2 B:GLU34 3.7 34.3 1.0
OE1 B:GLU34 3.8 44.4 1.0
CG B:GLU34 3.8 27.3 1.0
CB B:ASP35 4.3 23.0 1.0
O B:HOH286 5.0 48.0 1.0

Yttrium binding site 4 out of 4 in 4yhq

Go back to Yttrium Binding Sites List in 4yhq
Yttrium binding site 4 out of 4 in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A


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 Clinical Isolate PR20 with Grl-5010A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y102

b:14.8
occ:0.10
 O B:HOH272 1.2 18.5 0.3
Y B:Y1101 1.4 23.5 0.3
OD1 B:ASP35 2.6 31.4 1.0
O B:HOH210 2.9 17.7 0.7
O B:HOH234 3.5 24.7 0.3
CG B:ASP35 3.6 26.7 1.0
O B:HOH286 3.7 48.0 1.0
OD2 B:ASP35 3.9 36.8 1.0
CD B:GLU34 4.2 34.2 1.0
OE1 B:GLU34 4.3 44.4 1.0
CG B:GLU34 4.3 27.3 1.0
O B:HOH205 4.6 15.3 1.0
O B:HOH275 4.7 22.6 1.0
OE2 B:GLU34 4.8 34.3 1.0
CB B:ASP35 5.0 23.0 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 02:41:16 2020

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