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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:

Sodium (Na) 1 atom
Calcium (Ca) 1 atom

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.
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