Fluorine in PDB 8p41: Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator

Enzymatic activity of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator

All present enzymatic activity of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator:
3.2.1.104; 3.2.1.45;

Protein crystallography data

The structure of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator, PDB code: 8p41 was solved by M.-S.Schulze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.97 / 1.83
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 109.36, 285.53, 91.72, 90, 90, 90
R / Rfree (%) 20.5 / 23.8

Other elements in 8p41:

The structure of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator (pdb code 8p41). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator, PDB code: 8p41:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 8p41

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Fluorine binding site 1 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


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 Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:80.6
occ:0.83
 F24 A:WYC508 0.0 80.6 0.8
C23 A:WYC508 1.4 76.5 0.8
F25 A:WYC508 2.2 77.3 0.8
F26 A:WYC508 2.2 75.3 0.8
C21 A:WYC508 2.4 75.7 0.8
C22 A:WYC508 3.1 74.6 0.8
C20 A:WYC508 3.3 75.6 0.8
CD2 B:LEU287 3.9 26.9 1.0
C17 A:WYC508 4.4 73.7 0.8
C19 A:WYC508 4.5 73.8 0.8
CZ3 B:TRP291 4.9 24.2 1.0
C18 A:WYC508 4.9 73.2 0.8

Fluorine binding site 2 out of 12 in 8p41

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Fluorine binding site 2 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


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 Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:77.3
occ:0.83
 F25 A:WYC508 0.0 77.3 0.8
C23 A:WYC508 1.4 76.5 0.8
F26 A:WYC508 2.2 75.3 0.8
F24 A:WYC508 2.2 80.6 0.8
C21 A:WYC508 2.4 75.7 0.8
C20 A:WYC508 2.7 75.6 0.8
C22 A:WYC508 3.6 74.6 0.8
CD1 B:LEU240 3.9 28.0 1.0
C19 A:WYC508 4.1 73.8 0.8
CD B:PRO253 4.6 23.8 1.0
F29 A:WYC508 4.6 75.2 0.8
C17 A:WYC508 4.8 73.7 0.8
C18 A:WYC508 4.9 73.2 0.8
C27 A:WYC508 5.0 72.0 0.8

Fluorine binding site 3 out of 12 in 8p41

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Fluorine binding site 3 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


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 Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:75.3
occ:0.83
 F26 A:WYC508 0.0 75.3 0.8
C23 A:WYC508 1.4 76.5 0.8
F25 A:WYC508 2.2 77.3 0.8
F24 A:WYC508 2.2 80.6 0.8
C21 A:WYC508 2.4 75.7 0.8
C22 A:WYC508 2.9 74.6 0.8
CZ3 B:TRP291 3.3 24.2 1.0
C20 A:WYC508 3.5 75.6 0.8
CD1 B:LEU240 3.8 28.0 1.0
CD2 B:LEU287 4.0 26.9 1.0
CE3 B:TRP291 4.0 21.8 1.0
CB B:SER237 4.1 25.2 1.0
CD B:PRO253 4.1 23.8 1.0
CH2 B:TRP291 4.2 22.5 1.0
C17 A:WYC508 4.2 73.7 0.8
C19 A:WYC508 4.7 73.8 0.8
CA B:SER237 4.8 22.4 1.0
C18 A:WYC508 4.9 73.2 0.8

Fluorine binding site 4 out of 12 in 8p41

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Fluorine binding site 4 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


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 Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:71.3
occ:0.83
 F28 A:WYC508 0.0 71.3 0.8
C27 A:WYC508 1.4 72.0 0.8
F29 A:WYC508 2.2 75.2 0.8
F30 A:WYC508 2.2 70.6 0.8
C19 A:WYC508 2.4 73.8 0.8
C18 A:WYC508 3.0 73.2 0.8
O B:LEU240 3.3 27.1 1.0
C20 A:WYC508 3.3 75.6 0.8
CD2 B:LEU241 3.7 42.4 1.0
C B:LEU240 4.0 30.2 1.0
CB B:LEU240 4.0 24.7 1.0
C17 A:WYC508 4.3 73.7 0.8
C21 A:WYC508 4.5 75.7 0.8
N B:LEU241 4.6 27.8 1.0
CA B:LEU241 4.6 26.2 1.0
CG B:LEU241 4.6 31.3 1.0
CA B:LEU240 4.7 30.2 1.0
O B:HOH756 4.8 33.3 1.0
C22 A:WYC508 4.9 74.6 0.8

Fluorine binding site 5 out of 12 in 8p41

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Fluorine binding site 5 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:75.2
occ:0.83
 F29 A:WYC508 0.0 75.2 0.8
C27 A:WYC508 1.4 72.0 0.8
F28 A:WYC508 2.2 71.3 0.8
F30 A:WYC508 2.2 70.6 0.8
C19 A:WYC508 2.4 73.8 0.8
C20 A:WYC508 2.7 75.6 0.8
C18 A:WYC508 3.6 73.2 0.8
C21 A:WYC508 4.1 75.7 0.8
O4 A:SO4506 4.5 90.0 1.0
CD1 A:LEU317 4.6 59.8 1.0
F25 A:WYC508 4.6 77.3 0.8
C17 A:WYC508 4.7 73.7 0.8
O A:HOH802 4.9 48.0 1.0
C22 A:WYC508 4.9 74.6 0.8
C23 A:WYC508 5.0 76.5 0.8

Fluorine binding site 6 out of 12 in 8p41

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Fluorine binding site 6 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:70.6
occ:0.83
 F30 A:WYC508 0.0 70.6 0.8
C27 A:WYC508 1.4 72.0 0.8
F29 A:WYC508 2.2 75.2 0.8
F28 A:WYC508 2.2 71.3 0.8
C19 A:WYC508 2.4 73.8 0.8
C18 A:WYC508 2.9 73.2 0.8
CD1 A:LEU317 3.3 59.8 1.0
C20 A:WYC508 3.5 75.6 0.8
CD2 B:LEU241 4.2 42.4 1.0
C17 A:WYC508 4.2 73.7 0.8
O4 A:SO4506 4.3 90.0 1.0
CG A:LEU317 4.5 50.2 1.0
C21 A:WYC508 4.7 75.7 0.8
C22 A:WYC508 4.9 74.6 0.8

Fluorine binding site 7 out of 12 in 8p41

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Fluorine binding site 7 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:46.7
occ:1.00
 F24 A:WYC509 0.0 46.7 1.0
C23 A:WYC509 1.4 44.4 1.0
F26 A:WYC509 2.2 43.6 1.0
F25 A:WYC509 2.2 52.4 1.0
C21 A:WYC509 2.3 40.4 1.0
C22 A:WYC509 2.9 38.8 1.0
CD2 B:LEU314 3.0 29.0 1.0
C20 A:WYC509 3.3 38.1 1.0
CE1 A:PHE316 3.9 37.2 1.0
CZ A:PHE316 3.9 38.6 1.0
CE2 B:PHE316 4.0 33.1 1.0
CZ B:PHE316 4.1 38.5 1.0
CE2 B:TYR313 4.1 25.2 1.0
C17 A:WYC509 4.1 39.5 1.0
CD2 B:TYR313 4.2 27.8 1.0
CG B:LEU314 4.4 21.9 1.0
C19 A:WYC509 4.5 38.9 1.0
C18 A:WYC509 4.8 35.4 1.0

Fluorine binding site 8 out of 12 in 8p41

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Fluorine binding site 8 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:52.4
occ:1.00
 F25 A:WYC509 0.0 52.4 1.0
C23 A:WYC509 1.4 44.4 1.0
F26 A:WYC509 2.2 43.6 1.0
F24 A:WYC509 2.2 46.7 1.0
C21 A:WYC509 2.4 40.4 1.0
C20 A:WYC509 2.7 38.1 1.0
CE1 A:PHE316 3.3 37.2 1.0
CD2 B:LEU314 3.3 29.0 1.0
C6 A:WYC508 3.5 36.3 0.8
C22 A:WYC509 3.6 38.8 1.0
CL7 A:WYC508 3.7 37.1 0.8
C5 A:WYC508 3.7 33.9 0.8
CZ A:PHE316 3.9 38.6 1.0
C8 A:WYC508 4.0 36.2 0.8
C19 A:WYC509 4.0 38.9 1.0
CD1 B:LEU314 4.2 29.8 1.0
CG B:LEU314 4.3 21.9 1.0
C4 A:WYC508 4.3 40.3 0.8
CD1 A:PHE316 4.4 35.7 1.0
C9 A:WYC508 4.5 37.9 0.8
F30 A:WYC509 4.6 41.2 1.0
C10 A:WYC508 4.7 41.4 0.8
C17 A:WYC509 4.8 39.5 1.0
C27 A:WYC509 4.9 38.0 1.0
C18 A:WYC509 4.9 35.4 1.0
CD2 B:TYR313 5.0 27.8 1.0

Fluorine binding site 9 out of 12 in 8p41

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Fluorine binding site 9 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:43.6
occ:1.00
 F26 A:WYC509 0.0 43.6 1.0
C23 A:WYC509 1.4 44.4 1.0
F25 A:WYC509 2.2 52.4 1.0
F24 A:WYC509 2.2 46.7 1.0
C21 A:WYC509 2.4 40.4 1.0
C22 A:WYC509 3.0 38.8 1.0
CE2 B:TYR313 3.2 25.2 1.0
C9 A:WYC509 3.2 29.4 1.0
C20 A:WYC509 3.4 38.1 1.0
CD2 B:TYR313 3.5 27.8 1.0
C10 A:WYC509 3.5 33.1 1.0
C8 A:WYC509 3.6 29.8 1.0
O13 A:WYC509 3.9 33.0 1.0
N11 A:WYC509 4.0 35.3 1.0
CD2 B:LEU314 4.0 29.0 1.0
C6 A:WYC509 4.1 32.5 1.0
C4 A:WYC509 4.1 37.2 1.0
C12 A:WYC509 4.1 36.1 1.0
C17 A:WYC509 4.2 39.5 1.0
C5 A:WYC509 4.4 33.0 1.0
CZ B:TYR313 4.4 36.0 1.0
C19 A:WYC509 4.6 38.9 1.0
CL7 A:WYC508 4.8 37.1 0.8
OH B:TYR313 4.9 35.9 1.0
CG B:TYR313 4.9 29.0 1.0
C18 A:WYC509 4.9 35.4 1.0

Fluorine binding site 10 out of 12 in 8p41

Go back to Fluorine Binding Sites List in 8p41
Fluorine binding site 10 out of 12 in the Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Glucocerebrosidase in Complex with Allosteric Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F509

b:40.2
occ:1.00
 F28 A:WYC509 0.0 40.2 1.0
C27 A:WYC509 1.4 38.0 1.0
F29 A:WYC509 2.2 42.3 1.0
F30 A:WYC509 2.2 41.2 1.0
C19 A:WYC509 2.3 38.9 1.0
C18 A:WYC509 3.1 35.4 1.0
C20 A:WYC509 3.2 38.1 1.0
CB A:ASP315 3.6 27.9 1.0
CZ A:PHE316 3.6 38.6 1.0
CE2 A:PHE316 3.7 41.4 1.0
OD2 A:ASP315 3.9 29.0 1.0
CB A:SER345 4.0 31.1 1.0
CG A:ASP315 4.0 31.8 1.0
CE1 A:PHE316 4.3 37.2 1.0
C17 A:WYC509 4.4 39.5 1.0
C21 A:WYC509 4.4 40.4 1.0
CD2 A:PHE316 4.5 34.3 1.0
C A:SER345 4.6 31.2 1.0
N A:LYS346 4.6 21.8 1.0
O A:HOH655 4.8 29.5 1.0
CA A:SER345 4.8 29.1 1.0
C22 A:WYC509 4.9 38.8 1.0
O A:SER345 4.9 25.6 1.0
CA A:ASP315 4.9 26.0 1.0
OD1 A:ASP315 5.0 31.1 1.0

Reference:

M.E.D.Schulze, D.Scholz, E.Jnoff, A.Hall, J.Melin, Z.A.Sands, E.Rodriguez, V.M.Andre. Identification of Ss-Glucocerebrosidase Activators For Glucosylceramide Hydrolysis. Chemmedchem 00548 2024.
ISSN: ESSN 1860-7187
PubMed: 38381042
DOI: 10.1002/CMDC.202300548
Page generated: Fri Aug 2 21:42:29 2024

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