Fluorine in PDB 8ax3: Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
Enzymatic activity of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
All present enzymatic activity of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride:
3.2.1.104;
3.2.1.45;
Protein crystallography data
The structure of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride, PDB code: 8ax3
was solved by
R.J.Rowland,
G.J.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
51.82 /
1.59
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.92,
155.984,
68.036,
90,
101.96,
90
|
|
R / Rfree (%)
|
18.2 /
21.3
|
Other elements in 8ax3:
The structure of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
(pdb code 8ax3). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride, PDB code: 8ax3:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 8ax3
Go back to
Fluorine Binding Sites List in 8ax3
Fluorine binding site 1 out
of 4 in the Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F515
b:33.9
occ:1.00
|
F1
|
A:OD0515
|
0.0
|
33.9
|
1.0
|
|
C4
|
A:OD0515
|
1.4
|
31.8
|
1.0
|
|
H5
|
A:OD0515
|
1.9
|
32.3
|
1.0
|
|
C3
|
A:OD0515
|
2.4
|
32.2
|
1.0
|
|
C5
|
A:OD0515
|
2.4
|
32.0
|
1.0
|
|
H6
|
A:OD0515
|
2.5
|
31.8
|
1.0
|
|
HE1
|
A:HIS490
|
2.5
|
18.8
|
1.0
|
|
H4
|
A:OD0515
|
2.6
|
31.8
|
1.0
|
|
HE
|
A:ARG39
|
2.9
|
21.3
|
1.0
|
|
H
|
A:ILE483
|
2.9
|
20.4
|
1.0
|
|
O2
|
A:OD0515
|
3.0
|
29.5
|
1.0
|
|
O
|
A:ILE483
|
3.2
|
25.8
|
1.0
|
|
H7
|
A:OD0515
|
3.3
|
29.5
|
0.0
|
|
NE
|
A:ARG39
|
3.3
|
21.2
|
1.0
|
|
HB
|
A:ILE483
|
3.3
|
27.8
|
1.0
|
|
OG1
|
A:THR482
|
3.4
|
17.3
|
1.0
|
|
CE1
|
A:HIS490
|
3.4
|
18.2
|
1.0
|
|
C2
|
A:OD0515
|
3.5
|
31.2
|
1.0
|
|
HD11
|
A:ILE483
|
3.5
|
30.6
|
1.0
|
|
HH21
|
A:ARG39
|
3.5
|
22.3
|
1.0
|
|
HD3
|
A:ARG39
|
3.6
|
20.1
|
1.0
|
|
HG1
|
A:THR482
|
3.7
|
17.4
|
0.0
|
|
C6
|
A:OD0515
|
3.7
|
33.4
|
1.0
|
|
N
|
A:ILE483
|
3.7
|
20.4
|
1.0
|
|
CZ
|
A:ARG39
|
3.8
|
22.6
|
1.0
|
|
HH
|
A:TYR492
|
3.8
|
19.1
|
0.0
|
|
NH2
|
A:ARG39
|
3.8
|
22.3
|
1.0
|
|
HD3
|
A:PRO485
|
3.9
|
18.6
|
1.0
|
|
H8
|
A:OD0515
|
3.9
|
33.9
|
1.0
|
|
CD
|
A:ARG39
|
4.0
|
19.9
|
1.0
|
|
HG13
|
A:ILE483
|
4.0
|
29.8
|
1.0
|
|
CB
|
A:ILE483
|
4.0
|
28.5
|
1.0
|
|
C
|
A:ILE483
|
4.1
|
22.9
|
1.0
|
|
C1
|
A:OD0515
|
4.1
|
33.8
|
1.0
|
|
HD1
|
A:HIS490
|
4.1
|
18.8
|
0.0
|
|
H2
|
A:OD0515
|
4.2
|
33.5
|
1.0
|
|
CA
|
A:ILE483
|
4.2
|
22.6
|
1.0
|
|
ND1
|
A:HIS490
|
4.2
|
18.9
|
1.0
|
|
H3
|
A:OD0515
|
4.3
|
32.0
|
1.0
|
|
HD2
|
A:ARG39
|
4.3
|
20.1
|
1.0
|
|
CG1
|
A:ILE483
|
4.3
|
30.1
|
1.0
|
|
CD1
|
A:ILE483
|
4.3
|
30.8
|
1.0
|
|
OH
|
A:TYR492
|
4.3
|
19.0
|
1.0
|
|
NE2
|
A:HIS490
|
4.4
|
19.6
|
1.0
|
|
HA
|
A:THR482
|
4.4
|
18.2
|
1.0
|
|
HE2
|
A:HIS490
|
4.5
|
19.4
|
0.0
|
|
HH22
|
A:ARG39
|
4.5
|
22.4
|
1.0
|
|
HG3
|
A:PRO485
|
4.6
|
18.9
|
1.0
|
|
OE2
|
A:GLU41
|
4.7
|
20.9
|
1.0
|
|
CB
|
A:THR482
|
4.7
|
18.0
|
1.0
|
|
NH1
|
A:ARG39
|
4.7
|
22.7
|
1.0
|
|
C
|
A:THR482
|
4.8
|
18.6
|
1.0
|
|
CD
|
A:PRO485
|
4.8
|
18.7
|
1.0
|
|
O3
|
A:OD0515
|
4.8
|
37.2
|
1.0
|
|
CA
|
A:THR482
|
4.8
|
17.9
|
1.0
|
|
HD12
|
A:ILE483
|
4.9
|
30.6
|
1.0
|
|
H9
|
A:OD0515
|
4.9
|
37.3
|
0.0
|
|
HD13
|
A:ILE483
|
4.9
|
30.6
|
1.0
|
|
HG2
|
A:PRO485
|
5.0
|
18.9
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 8ax3
Go back to
Fluorine Binding Sites List in 8ax3
Fluorine binding site 2 out
of 4 in the Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F518
b:19.7
occ:1.00
|
F1
|
A:OD0518
|
0.0
|
19.7
|
1.0
|
|
C4
|
A:OD0518
|
1.4
|
15.7
|
1.0
|
|
H5
|
A:OD0518
|
1.9
|
16.6
|
1.0
|
|
HD21
|
A:ASN396
|
2.3
|
20.7
|
1.0
|
|
C5
|
A:OD0518
|
2.3
|
15.9
|
1.0
|
|
C3
|
A:OD0518
|
2.3
|
16.4
|
1.0
|
|
H6
|
A:OD0518
|
2.4
|
15.7
|
1.0
|
|
H4
|
A:OD0518
|
2.5
|
16.2
|
1.0
|
|
O2
|
A:OD0518
|
2.8
|
15.1
|
1.0
|
|
HB2
|
A:SER345
|
2.9
|
20.5
|
1.0
|
|
HB3
|
A:SER345
|
3.0
|
20.5
|
1.0
|
|
H7
|
A:OD0518
|
3.1
|
15.1
|
0.0
|
|
ND2
|
A:ASN396
|
3.1
|
20.7
|
1.0
|
|
CB
|
A:SER345
|
3.4
|
20.6
|
1.0
|
|
HD22
|
A:ASN396
|
3.4
|
20.7
|
1.0
|
|
HG12
|
A:VAL398
|
3.5
|
14.8
|
1.0
|
|
C2
|
A:OD0518
|
3.5
|
16.3
|
1.0
|
|
C6
|
A:OD0518
|
3.7
|
15.6
|
1.0
|
|
HG
|
A:SER345
|
3.7
|
20.8
|
0.0
|
|
H8
|
A:OD0518
|
4.0
|
15.6
|
1.0
|
|
C1
|
A:OD0518
|
4.1
|
16.2
|
1.0
|
|
HE2
|
A:PHE128
|
4.1
|
14.8
|
1.0
|
|
OG
|
A:SER345
|
4.1
|
20.9
|
1.0
|
|
HE1
|
A:TRP381
|
4.1
|
13.2
|
1.0
|
|
CG
|
A:ASN396
|
4.2
|
20.6
|
1.0
|
|
H3
|
A:OD0518
|
4.2
|
16.3
|
1.0
|
|
HH
|
A:TYR313
|
4.2
|
15.6
|
0.0
|
|
HG
|
A:CYS342
|
4.2
|
15.4
|
0.0
|
|
HG13
|
A:VAL398
|
4.2
|
14.8
|
1.0
|
|
CG1
|
A:VAL398
|
4.2
|
14.8
|
1.0
|
|
SG
|
A:CYS342
|
4.4
|
15.3
|
1.0
|
|
HE1
|
A:TYR313
|
4.4
|
14.7
|
1.0
|
|
HZ
|
A:PHE246
|
4.4
|
17.5
|
1.0
|
|
H2
|
A:OD0518
|
4.4
|
15.9
|
1.0
|
|
OD1
|
A:ASN396
|
4.4
|
21.5
|
1.0
|
|
OD2
|
A:ASP127
|
4.5
|
16.4
|
1.0
|
|
OH
|
A:TYR313
|
4.5
|
15.6
|
1.0
|
|
HA
|
A:SER345
|
4.5
|
20.0
|
1.0
|
|
HG11
|
A:VAL398
|
4.5
|
14.8
|
1.0
|
|
CE1
|
A:TYR313
|
4.6
|
14.9
|
1.0
|
|
CA
|
A:SER345
|
4.6
|
20.0
|
1.0
|
|
CZ
|
A:TYR313
|
4.7
|
14.5
|
1.0
|
|
NE1
|
A:TRP381
|
4.7
|
13.2
|
1.0
|
|
HD1
|
A:TRP381
|
4.7
|
13.1
|
1.0
|
|
O3
|
A:OD0518
|
4.7
|
14.6
|
1.0
|
|
H9
|
A:OD0518
|
4.9
|
14.7
|
0.0
|
|
HG22
|
A:VAL398
|
4.9
|
15.5
|
1.0
|
|
OE2
|
A:GLU340
|
5.0
|
15.3
|
1.0
|
|
CD1
|
A:TRP381
|
5.0
|
13.1
|
1.0
|
|
HE2
|
A:PHE246
|
5.0
|
17.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 8ax3
Go back to
Fluorine Binding Sites List in 8ax3
Fluorine binding site 3 out
of 4 in the Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F515
b:33.4
occ:1.00
|
F1
|
B:OD0515
|
0.0
|
33.4
|
1.0
|
|
C4
|
B:OD0515
|
1.4
|
34.5
|
1.0
|
|
H5
|
B:OD0515
|
1.9
|
34.2
|
1.0
|
|
C3
|
B:OD0515
|
2.4
|
35.2
|
1.0
|
|
C5
|
B:OD0515
|
2.4
|
33.3
|
1.0
|
|
H6
|
B:OD0515
|
2.5
|
33.6
|
1.0
|
|
H4
|
B:OD0515
|
2.6
|
35.0
|
1.0
|
|
HE1
|
B:HIS490
|
2.7
|
17.7
|
1.0
|
|
HG23
|
B:ILE483
|
2.7
|
31.3
|
1.0
|
|
HE
|
B:ARG39
|
2.9
|
23.0
|
1.0
|
|
H
|
B:ILE483
|
2.9
|
22.3
|
1.0
|
|
O2
|
B:OD0515
|
2.9
|
31.6
|
1.0
|
|
NE
|
B:ARG39
|
3.2
|
23.1
|
1.0
|
|
O
|
B:ILE483
|
3.2
|
27.5
|
1.0
|
|
H7
|
B:OD0515
|
3.2
|
31.6
|
0.0
|
|
HG21
|
B:ILE483
|
3.3
|
31.3
|
1.0
|
|
OG1
|
B:THR482
|
3.3
|
19.2
|
1.0
|
|
CG2
|
B:ILE483
|
3.4
|
31.7
|
1.0
|
|
HH21
|
B:ARG39
|
3.4
|
23.5
|
1.0
|
|
HD3
|
B:ARG39
|
3.4
|
22.6
|
1.0
|
|
C2
|
B:OD0515
|
3.5
|
35.1
|
1.0
|
|
HG1
|
B:THR482
|
3.5
|
19.1
|
0.0
|
|
CE1
|
B:HIS490
|
3.5
|
17.6
|
1.0
|
|
CZ
|
B:ARG39
|
3.5
|
23.1
|
1.0
|
|
NH2
|
B:ARG39
|
3.6
|
23.7
|
1.0
|
|
HH
|
B:TYR492
|
3.7
|
21.6
|
0.0
|
|
C6
|
B:OD0515
|
3.7
|
35.7
|
1.0
|
|
N
|
B:ILE483
|
3.8
|
22.0
|
1.0
|
|
CD
|
B:ARG39
|
3.8
|
22.6
|
1.0
|
|
H8
|
B:OD0515
|
3.9
|
35.3
|
1.0
|
|
HG22
|
B:ILE483
|
4.0
|
31.3
|
1.0
|
|
HD2
|
B:ARG39
|
4.1
|
22.6
|
1.0
|
|
HD3
|
B:PRO485
|
4.1
|
20.7
|
1.0
|
|
C1
|
B:OD0515
|
4.1
|
35.1
|
1.0
|
|
C
|
B:ILE483
|
4.1
|
24.6
|
1.0
|
|
H3
|
B:OD0515
|
4.2
|
35.1
|
1.0
|
|
HD1
|
B:HIS490
|
4.3
|
17.7
|
0.0
|
|
HH22
|
B:ARG39
|
4.3
|
23.5
|
1.0
|
|
ND1
|
B:HIS490
|
4.3
|
17.8
|
1.0
|
|
H2
|
B:OD0515
|
4.3
|
35.1
|
1.0
|
|
OH
|
B:TYR492
|
4.3
|
21.8
|
1.0
|
|
CA
|
B:ILE483
|
4.3
|
24.9
|
1.0
|
|
CB
|
B:ILE483
|
4.4
|
30.4
|
1.0
|
|
NH1
|
B:ARG39
|
4.4
|
22.5
|
1.0
|
|
HA
|
B:THR482
|
4.4
|
19.5
|
1.0
|
|
NE2
|
B:HIS490
|
4.5
|
17.9
|
1.0
|
|
HE2
|
B:HIS490
|
4.6
|
17.8
|
0.0
|
|
CB
|
B:THR482
|
4.6
|
18.8
|
1.0
|
|
HH11
|
B:ARG39
|
4.7
|
22.7
|
1.0
|
|
OE2
|
B:GLU41
|
4.7
|
20.1
|
1.0
|
|
C
|
B:THR482
|
4.8
|
20.5
|
1.0
|
|
O3
|
B:OD0515
|
4.8
|
36.7
|
1.0
|
|
CA
|
B:THR482
|
4.8
|
19.1
|
1.0
|
|
HG3
|
B:PRO485
|
4.9
|
20.8
|
1.0
|
|
H9
|
B:OD0515
|
4.9
|
36.8
|
0.0
|
|
HH12
|
B:ARG39
|
4.9
|
22.7
|
1.0
|
|
CD
|
B:PRO485
|
5.0
|
21.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 8ax3
Go back to
Fluorine Binding Sites List in 8ax3
Fluorine binding site 4 out
of 4 in the Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Recombinant Human Beta-Glucocerebrosidase in Complex with L-Carbaxylosyl Fluoride within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F516
b:20.1
occ:1.00
|
F1
|
B:OD0516
|
0.0
|
20.1
|
1.0
|
|
C4
|
B:OD0516
|
1.4
|
19.4
|
1.0
|
|
H5
|
B:OD0516
|
1.9
|
19.4
|
1.0
|
|
HD21
|
B:ASN396
|
2.2
|
20.2
|
1.0
|
|
C5
|
B:OD0516
|
2.3
|
18.8
|
1.0
|
|
C3
|
B:OD0516
|
2.4
|
19.4
|
1.0
|
|
H6
|
B:OD0516
|
2.4
|
18.9
|
1.0
|
|
H4
|
B:OD0516
|
2.6
|
19.5
|
1.0
|
|
O2
|
B:OD0516
|
2.9
|
19.6
|
1.0
|
|
HB2
|
B:SER345
|
2.9
|
21.0
|
1.0
|
|
HB3
|
B:SER345
|
2.9
|
21.0
|
1.0
|
|
ND2
|
B:ASN396
|
3.1
|
19.9
|
1.0
|
|
H7
|
B:OD0516
|
3.2
|
19.7
|
0.0
|
|
HG12
|
B:VAL398
|
3.3
|
15.1
|
1.0
|
|
CB
|
B:SER345
|
3.4
|
21.3
|
1.0
|
|
HD22
|
B:ASN396
|
3.4
|
20.2
|
1.0
|
|
C2
|
B:OD0516
|
3.5
|
19.8
|
1.0
|
|
C6
|
B:OD0516
|
3.7
|
18.3
|
1.0
|
|
HG
|
B:SER345
|
3.8
|
20.2
|
0.0
|
|
HE2
|
B:PHE128
|
4.0
|
16.2
|
1.0
|
|
H8
|
B:OD0516
|
4.0
|
18.2
|
1.0
|
|
C1
|
B:OD0516
|
4.1
|
19.1
|
1.0
|
|
HG13
|
B:VAL398
|
4.1
|
15.1
|
1.0
|
|
CG1
|
B:VAL398
|
4.1
|
15.1
|
1.0
|
|
CG
|
B:ASN396
|
4.1
|
20.8
|
1.0
|
|
OG
|
B:SER345
|
4.1
|
20.2
|
1.0
|
|
HG
|
B:CYS342
|
4.2
|
17.6
|
0.0
|
|
H3
|
B:OD0516
|
4.2
|
19.6
|
1.0
|
|
HE1
|
B:TRP381
|
4.2
|
15.6
|
1.0
|
|
SG
|
B:CYS342
|
4.3
|
17.6
|
1.0
|
|
H2
|
B:OD0516
|
4.4
|
18.9
|
1.0
|
|
OD1
|
B:ASN396
|
4.4
|
23.0
|
1.0
|
|
HA
|
B:SER345
|
4.4
|
21.3
|
1.0
|
|
HG11
|
B:VAL398
|
4.4
|
15.1
|
1.0
|
|
HZ
|
B:PHE246
|
4.4
|
19.7
|
1.0
|
|
O
|
B:HOH651
|
4.4
|
35.4
|
1.0
|
|
HH
|
B:TYR313
|
4.4
|
14.5
|
0.0
|
|
OD2
|
B:ASP127
|
4.4
|
17.1
|
1.0
|
|
HE1
|
B:TYR313
|
4.5
|
14.2
|
1.0
|
|
CA
|
B:SER345
|
4.5
|
21.0
|
1.0
|
|
OH
|
B:TYR313
|
4.6
|
14.4
|
1.0
|
|
CE1
|
B:TYR313
|
4.7
|
14.0
|
1.0
|
|
HD1
|
B:TRP381
|
4.7
|
15.3
|
1.0
|
|
O3
|
B:OD0516
|
4.7
|
16.9
|
1.0
|
|
NE1
|
B:TRP381
|
4.8
|
16.0
|
1.0
|
|
CZ
|
B:TYR313
|
4.8
|
14.3
|
1.0
|
|
HE2
|
B:PHE246
|
4.8
|
19.6
|
1.0
|
|
HG22
|
B:VAL398
|
4.8
|
15.1
|
1.0
|
|
H9
|
B:OD0516
|
4.8
|
17.0
|
0.0
|
|
CE2
|
B:PHE128
|
4.9
|
16.2
|
1.0
|
|
Reference:
S.Bhosale,
S.Kandalkar,
P.A.Gilormini,
O.Akintola,
R.J.Rowland,
P.J.P.Adabala,
D.King,
M.C.Deen,
K.Xi,
G.J.Davies,
D.J.Vocadlo,
A.J.Bennet.
Single Turnover Covalent Inhibitors For Functional Chaperoning of Lysosomal Glycoside Hydrolases To Be Published.
Page generated: Fri Aug 2 16:34:00 2024
|
