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Fluorine 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:

Yttrium (Y) 4 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Multidrug Resistant Clinical Isolate PR20 with Grl-5010A, PDB code: 4yhq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4yhq

Go back to Fluorine Binding Sites List in 4yhq
Fluorine 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 Fluorine with other atoms in the F 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:F201

b:14.3
occ:0.50
 F39 A:G10201 0.0 14.3 0.5
C30 A:G10201 1.4 12.7 0.5
O A:GLY48 2.1 15.7 0.5
F40 A:G10201 2.1 16.1 0.5
C29 A:G10201 2.4 13.1 0.5
C31 A:G10201 2.4 12.4 0.5
O23 A:G10201 2.8 11.7 0.5
C6 A:G10201 2.8 9.6 0.5
C24 A:G10201 2.8 11.5 0.5
C21 A:G10201 2.9 10.3 0.5
C12 A:G10201 3.1 12.9 0.5
O22 A:G10201 3.2 10.8 0.5
C35 A:G10201 3.2 14.4 0.5
O A:HOH303 3.3 17.0 0.5
C34 A:G10201 3.3 14.0 0.5
C A:GLY48 3.3 14.9 0.5
O A:GLY48 3.4 15.4 0.5
C36 A:G10201 3.4 14.2 0.5
C7 A:G10201 3.4 12.3 0.5
O28 A:G10201 3.5 11.6 0.5
N20 A:G10201 3.5 9.4 0.5
C33 A:G10201 3.5 11.2 0.5
C27 A:G10201 3.6 12.2 0.5
C A:GLY48 3.6 15.6 0.5
C37 A:G10201 3.6 14.1 0.5
O10 A:G10201 3.7 12.0 0.5
CA A:GLY49 3.7 13.1 0.5
C38 A:G10201 3.7 11.1 0.5
C5 A:G10201 3.8 8.0 0.5
N A:GLY49 3.9 14.6 0.5
C15 A:G10201 3.9 13.9 0.5
CA A:GLY49 4.0 16.4 0.5
C13 A:G10201 4.0 9.6 0.5
S8 A:G10201 4.1 10.5 0.5
N11 A:G10201 4.1 9.9 0.5
N A:GLY49 4.2 14.3 0.5
O A:HOH341 4.3 33.5 1.0
C25 A:G10201 4.3 13.2 0.5
CA A:GLY48 4.3 15.8 0.5
N A:GLY48 4.4 16.7 0.5
C A:GLY49 4.4 14.5 0.5
O26 A:G10201 4.4 13.1 0.5
C19 A:G10201 4.5 10.3 0.5
CA A:GLY48 4.5 16.1 0.5
O A:HOH375 4.7 38.5 1.0
C32 A:G10201 4.7 10.8 0.5
C2 A:G10201 4.7 10.3 0.5
C14 A:G10201 4.8 13.3 0.5
O A:GLY49 4.8 16.1 0.5
C4 A:G10201 4.9 8.8 0.5
O A:GLY27 4.9 12.9 1.0

Fluorine binding site 2 out of 4 in 4yhq

Go back to Fluorine Binding Sites List in 4yhq
Fluorine 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 Fluorine with other atoms in the F 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:F201

b:13.2
occ:0.50
 F39 A:G10201 0.0 13.2 0.5
O B:HOH212 1.0 28.5 0.5
C30 A:G10201 1.4 12.2 0.5
O B:GLY48 2.1 16.4 0.6
F40 A:G10201 2.1 15.6 0.5
C31 A:G10201 2.4 11.2 0.5
C29 A:G10201 2.4 13.4 0.5
C6 A:G10201 2.7 12.2 0.5
O23 A:G10201 2.8 10.5 0.5
C24 A:G10201 2.8 10.3 0.5
C21 A:G10201 2.9 10.4 0.5
C12 A:G10201 3.1 13.0 0.5
O22 A:G10201 3.1 10.4 0.5
C35 A:G10201 3.3 12.5 0.5
C B:GLY48 3.3 12.6 0.6
O B:GLY48 3.3 13.6 0.4
O A:HOH302 3.3 16.6 0.5
C34 A:G10201 3.3 12.6 0.5
C7 A:G10201 3.4 12.8 0.5
C36 A:G10201 3.4 12.2 0.5
N20 A:G10201 3.5 8.4 0.5
O28 A:G10201 3.5 10.8 0.5
O10 A:G10201 3.5 12.1 0.5
C33 A:G10201 3.6 11.1 0.5
C27 A:G10201 3.6 11.6 0.5
C37 A:G10201 3.6 12.2 0.5
C B:GLY48 3.7 13.2 0.4
CA B:GLY49 3.7 13.3 0.5
C5 A:G10201 3.7 10.1 0.5
C38 A:G10201 3.8 9.2 0.5
N B:GLY49 3.9 14.4 0.5
C15 A:G10201 4.0 14.7 0.5
CA B:GLY49 4.0 14.8 0.5
S8 A:G10201 4.0 10.8 0.5
N11 A:G10201 4.0 10.3 0.5
C13 A:G10201 4.0 11.5 0.5
N B:GLY49 4.1 12.6 0.5
O B:HOH238 4.2 23.6 0.5
C25 A:G10201 4.3 9.9 0.5
CA B:GLY48 4.3 15.9 0.6
N B:GLY48 4.3 15.3 0.6
C19 A:G10201 4.4 9.6 0.5
O26 A:G10201 4.4 11.5 0.5
C B:GLY49 4.5 14.5 0.5
CA B:GLY48 4.6 15.1 0.4
C2 A:G10201 4.7 11.8 0.5
C32 A:G10201 4.7 10.6 0.5
C14 A:G10201 4.7 15.2 0.5
O B:HOH271 4.9 35.0 1.0
O B:GLY49 4.9 16.4 0.5
C4 A:G10201 4.9 10.3 0.5
O B:GLY27 5.0 12.7 1.0

Fluorine binding site 3 out of 4 in 4yhq

Go back to Fluorine Binding Sites List in 4yhq
Fluorine 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 Fluorine with other atoms in the F 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
A:F201

b:16.1
occ:0.50
 F40 A:G10201 0.0 16.1 0.5
C30 A:G10201 1.3 12.7 0.5
F39 A:G10201 2.1 14.3 0.5
C31 A:G10201 2.2 12.4 0.5
O A:HOH341 2.4 33.5 1.0
C29 A:G10201 2.4 13.1 0.5
O A:GLY48 2.9 15.7 0.5
C27 A:G10201 3.0 12.2 0.5
O28 A:G10201 3.0 11.6 0.5
C24 A:G10201 3.6 11.5 0.5
O A:HOH303 3.6 17.0 0.5
C7 A:G10201 3.7 12.3 0.5
O A:GLY48 3.7 15.4 0.5
C A:GLY48 3.8 15.6 0.5
C6 A:G10201 3.8 9.6 0.5
N A:GLY48 3.8 16.7 0.5
C A:GLY48 3.9 14.9 0.5
CA A:GLY48 3.9 16.1 0.5
O23 A:G10201 4.1 11.7 0.5
CA A:GLY48 4.2 15.8 0.5
C35 A:G10201 4.2 14.4 0.5
NH2 B:ARG8 4.2 15.6 0.2
C34 A:G10201 4.3 14.0 0.5
N A:GLY48 4.3 17.5 0.5
O26 A:G10201 4.3 13.1 0.5
N A:GLY49 4.4 14.6 0.5
O A:HOH375 4.5 38.5 1.0
OD2 A:ASP29 4.6 23.2 1.0
C25 A:G10201 4.6 13.2 0.5
C21 A:G10201 4.7 10.3 0.5
C33 A:G10201 4.9 11.2 0.5
C36 A:G10201 4.9 14.2 0.5
CA A:GLY49 4.9 13.1 0.5
C A:VAL47 4.9 17.3 0.5
C2 A:G10201 5.0 10.3 0.5

Fluorine binding site 4 out of 4 in 4yhq

Go back to Fluorine Binding Sites List in 4yhq
Fluorine 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 Fluorine with other atoms in the F 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
A:F201

b:15.6
occ:0.50
 F40 A:G10201 0.0 15.6 0.5
C30 A:G10201 1.3 12.2 0.5
O B:HOH212 1.4 28.5 0.5
F39 A:G10201 2.1 13.2 0.5
C31 A:G10201 2.3 11.2 0.5
C29 A:G10201 2.3 13.4 0.5
O B:HOH238 2.3 23.6 0.5
O B:GLY48 2.9 16.4 0.6
C27 A:G10201 3.0 11.6 0.5
O28 A:G10201 3.0 10.8 0.5
O A:HOH302 3.6 16.6 0.5
C24 A:G10201 3.6 10.3 0.5
C7 A:G10201 3.7 12.8 0.5
O B:GLY48 3.7 13.6 0.4
C6 A:G10201 3.8 12.2 0.5
N B:GLY48 3.9 15.3 0.6
C B:GLY48 3.9 13.2 0.4
C B:GLY48 3.9 12.6 0.6
O23 A:G10201 4.1 10.5 0.5
CA B:GLY48 4.1 15.1 0.4
C35 A:G10201 4.2 12.5 0.5
C34 A:G10201 4.2 12.6 0.5
N B:GLY48 4.3 14.9 0.4
CA B:GLY48 4.3 15.9 0.6
O26 A:G10201 4.3 11.5 0.5
NH1 A:ARG8 4.5 29.8 0.5
OD2 B:ASP29 4.5 23.1 1.0
N B:GLY49 4.6 14.4 0.5
O B:HOH271 4.6 35.0 1.0
C25 A:G10201 4.6 9.9 0.5
C21 A:G10201 4.7 10.4 0.5
C36 A:G10201 4.9 12.2 0.5
C33 A:G10201 4.9 11.1 0.5
C2 A:G10201 4.9 11.8 0.5
CB B:VAL47 5.0 15.3 0.5
C B:VAL47 5.0 14.0 0.5

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: Sun Dec 13 12:15:55 2020

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