Fluorine in PDB 2wvs: Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
Protein crystallography data
The structure of Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant, PDB code: 2wvs
was solved by
A.Lammerts Van Bueren,
A.Ardevol,
J.Fayers-Kerr,
B.Luo,
Y.Zhang,
M.Sollogoub,
Y.Bleriot,
C.Rovira,
G.J.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
97.56 /
2.19
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.840,
185.160,
97.870,
90.00,
94.57,
90.00
|
R / Rfree (%)
|
17.8 /
23.5
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
(pdb code 2wvs). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant, PDB code: 2wvs:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 2wvs
Go back to
Fluorine Binding Sites List in 2wvs
Fluorine binding site 1 out
of 5 in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
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 An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1449
b:35.1
occ:1.00
|
F2
|
A:FUF1449
|
0.0
|
35.1
|
1.0
|
C2
|
A:FUF1449
|
1.4
|
31.5
|
1.0
|
C3
|
A:FUF1449
|
2.4
|
30.5
|
1.0
|
C1
|
A:FUF1449
|
2.4
|
30.5
|
1.0
|
O3
|
A:FUF1449
|
3.0
|
30.0
|
1.0
|
CH2
|
A:TRP232
|
3.2
|
36.9
|
1.0
|
NE1
|
A:TRP88
|
3.2
|
28.2
|
1.0
|
NE2
|
A:HIS136
|
3.3
|
20.9
|
1.0
|
OD2
|
A:ASP229
|
3.4
|
28.9
|
1.0
|
O5
|
A:FUF1449
|
3.5
|
29.1
|
1.0
|
CZ2
|
A:TRP88
|
3.6
|
31.2
|
1.0
|
C4
|
A:FUF1449
|
3.7
|
28.0
|
1.0
|
CE2
|
A:TRP88
|
3.8
|
29.8
|
1.0
|
CZ2
|
A:TRP232
|
3.9
|
36.6
|
1.0
|
CE1
|
A:HIS136
|
4.1
|
24.2
|
1.0
|
C5
|
A:FUF1449
|
4.1
|
27.9
|
1.0
|
CZ3
|
A:TRP232
|
4.2
|
35.7
|
1.0
|
CG
|
A:ASP229
|
4.2
|
24.8
|
1.0
|
OD1
|
A:ASP229
|
4.2
|
23.3
|
1.0
|
O4
|
A:FUF1449
|
4.3
|
26.1
|
1.0
|
CD2
|
A:HIS136
|
4.3
|
24.1
|
1.0
|
O
|
A:HOH2029
|
4.4
|
30.3
|
1.0
|
CD1
|
A:TRP88
|
4.4
|
29.0
|
1.0
|
CE1
|
A:HIS135
|
4.9
|
24.3
|
1.0
|
CH2
|
A:TRP88
|
4.9
|
31.7
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 2wvs
Go back to
Fluorine Binding Sites List in 2wvs
Fluorine binding site 2 out
of 5 in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
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 An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1450
b:29.9
occ:0.60
|
F2
|
A:FUF1450
|
0.0
|
29.9
|
0.6
|
C2
|
A:FUF1450
|
1.4
|
28.4
|
0.6
|
C1
|
A:FUF1450
|
2.4
|
29.2
|
0.6
|
C3
|
A:FUF1450
|
2.4
|
27.9
|
0.6
|
OD1
|
A:ASP105
|
2.6
|
24.6
|
1.0
|
O
|
A:HOH2221
|
2.6
|
53.1
|
1.0
|
O1
|
A:FUF1450
|
2.8
|
30.3
|
0.6
|
O3
|
A:FUF1450
|
2.8
|
26.0
|
0.6
|
OD2
|
A:ASP105
|
3.1
|
30.8
|
1.0
|
CG
|
A:ASP105
|
3.2
|
26.6
|
1.0
|
O5
|
A:FUF1450
|
3.6
|
28.5
|
0.6
|
C4
|
A:FUF1450
|
3.7
|
24.8
|
0.6
|
C5
|
A:FUF1450
|
4.1
|
27.1
|
0.6
|
O4
|
A:FUF1450
|
4.2
|
23.5
|
0.6
|
CA
|
A:LYS102
|
4.7
|
28.0
|
1.0
|
CB
|
A:ASP105
|
4.7
|
25.4
|
1.0
|
CG
|
A:LYS102
|
4.8
|
33.1
|
1.0
|
O
|
A:LYS102
|
4.9
|
27.1
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 2wvs
Go back to
Fluorine Binding Sites List in 2wvs
Fluorine binding site 3 out
of 5 in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
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 An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1449
b:30.5
occ:1.00
|
F2
|
B:FUF1449
|
0.0
|
30.5
|
1.0
|
C2
|
B:FUF1449
|
1.4
|
28.0
|
1.0
|
C3
|
B:FUF1449
|
2.4
|
25.8
|
1.0
|
C1
|
B:FUF1449
|
2.5
|
28.1
|
1.0
|
O3
|
B:FUF1449
|
2.9
|
22.8
|
1.0
|
NE2
|
B:HIS136
|
3.3
|
25.5
|
1.0
|
O5
|
B:FUF1449
|
3.3
|
28.5
|
1.0
|
NE1
|
B:TRP88
|
3.3
|
21.9
|
1.0
|
OD2
|
B:ASP229
|
3.3
|
26.5
|
1.0
|
CH2
|
B:TRP232
|
3.7
|
26.7
|
1.0
|
CZ2
|
B:TRP88
|
3.7
|
18.9
|
1.0
|
C4
|
B:FUF1449
|
3.7
|
25.8
|
1.0
|
CE2
|
B:TRP88
|
3.9
|
22.7
|
1.0
|
CE1
|
B:HIS136
|
3.9
|
25.5
|
1.0
|
C5
|
B:FUF1449
|
4.1
|
27.4
|
1.0
|
CG
|
B:ASP229
|
4.1
|
22.2
|
1.0
|
OD1
|
B:ASP229
|
4.2
|
25.5
|
1.0
|
CZ3
|
B:TRP232
|
4.3
|
24.3
|
1.0
|
O4
|
B:FUF1449
|
4.3
|
23.2
|
1.0
|
CD2
|
B:HIS136
|
4.4
|
22.6
|
1.0
|
CD1
|
B:TRP88
|
4.5
|
23.0
|
1.0
|
NH1
|
B:ARG262
|
4.6
|
44.5
|
1.0
|
CZ2
|
B:TRP232
|
4.7
|
26.8
|
1.0
|
CE1
|
B:HIS135
|
4.9
|
20.7
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 2wvs
Go back to
Fluorine Binding Sites List in 2wvs
Fluorine binding site 4 out
of 5 in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
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 An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1449
b:37.6
occ:1.00
|
F2
|
C:FUF1449
|
0.0
|
37.6
|
1.0
|
C2
|
C:FUF1449
|
1.4
|
40.0
|
1.0
|
C3
|
C:FUF1449
|
2.4
|
39.7
|
1.0
|
C1
|
C:FUF1449
|
2.5
|
39.4
|
1.0
|
NE1
|
C:TRP88
|
2.9
|
22.6
|
1.0
|
O3
|
C:FUF1449
|
3.0
|
42.8
|
1.0
|
NE2
|
C:HIS136
|
3.1
|
21.5
|
1.0
|
O5
|
C:FUF1449
|
3.3
|
40.3
|
1.0
|
CZ2
|
C:TRP88
|
3.6
|
24.0
|
1.0
|
CE2
|
C:TRP88
|
3.6
|
22.7
|
1.0
|
OD2
|
C:ASP229
|
3.6
|
32.4
|
1.0
|
C4
|
C:FUF1449
|
3.7
|
40.0
|
1.0
|
CH2
|
C:TRP232
|
3.7
|
31.4
|
1.0
|
C5
|
C:FUF1449
|
3.9
|
40.3
|
1.0
|
CE1
|
C:HIS136
|
4.0
|
21.1
|
1.0
|
CD2
|
C:HIS136
|
4.0
|
23.6
|
1.0
|
CD1
|
C:TRP88
|
4.1
|
22.2
|
1.0
|
O4
|
C:FUF1449
|
4.3
|
38.5
|
1.0
|
CZ3
|
C:TRP232
|
4.3
|
34.0
|
1.0
|
CG
|
C:ASP229
|
4.4
|
25.9
|
1.0
|
OD1
|
C:ASP229
|
4.5
|
26.4
|
1.0
|
CZ2
|
C:TRP232
|
4.7
|
31.5
|
1.0
|
CE1
|
C:HIS135
|
4.8
|
24.8
|
1.0
|
CH2
|
C:TRP88
|
4.9
|
24.2
|
1.0
|
CD2
|
C:TRP88
|
4.9
|
23.0
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 2wvs
Go back to
Fluorine Binding Sites List in 2wvs
Fluorine binding site 5 out
of 5 in the Crystal Structure of An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant
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 An Alpha-L-Fucosidase GH29 Trapped Covalent Intermediate From Bacteroides Thetaiotaomicron in Complex with 2-Fluoro-Fucosyl Fluoride Using An E288Q Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1449
b:38.8
occ:1.00
|
F2
|
D:FUF1449
|
0.0
|
38.8
|
1.0
|
C2
|
D:FUF1449
|
1.4
|
38.5
|
1.0
|
C3
|
D:FUF1449
|
2.4
|
38.6
|
1.0
|
C1
|
D:FUF1449
|
2.4
|
37.8
|
1.0
|
O3
|
D:FUF1449
|
2.9
|
38.2
|
1.0
|
NE1
|
D:TRP88
|
3.0
|
34.9
|
1.0
|
NE2
|
D:HIS136
|
3.4
|
26.6
|
1.0
|
O5
|
D:FUF1449
|
3.4
|
37.0
|
1.0
|
OD2
|
D:ASP229
|
3.5
|
38.4
|
1.0
|
CZ2
|
D:TRP88
|
3.5
|
37.2
|
1.0
|
CE2
|
D:TRP88
|
3.6
|
36.3
|
1.0
|
C4
|
D:FUF1449
|
3.7
|
37.2
|
1.0
|
O
|
D:HOH2195
|
3.9
|
35.2
|
1.0
|
CH2
|
D:TRP232
|
4.0
|
46.2
|
1.0
|
C5
|
D:FUF1449
|
4.1
|
36.7
|
1.0
|
CD2
|
D:HIS136
|
4.2
|
28.6
|
1.0
|
O4
|
D:FUF1449
|
4.2
|
37.2
|
1.0
|
CD1
|
D:TRP88
|
4.2
|
34.4
|
1.0
|
CG
|
D:ASP229
|
4.3
|
33.4
|
1.0
|
CE1
|
D:HIS136
|
4.3
|
27.2
|
1.0
|
OD1
|
D:ASP229
|
4.3
|
33.7
|
1.0
|
CZ3
|
D:TRP232
|
4.4
|
44.1
|
1.0
|
CE1
|
D:HIS135
|
4.7
|
34.3
|
1.0
|
CH2
|
D:TRP88
|
4.8
|
37.0
|
1.0
|
CD2
|
D:TRP88
|
4.9
|
34.7
|
1.0
|
|
Reference:
A.Lammerts Van Bueren,
A.Ardevol,
J.Fayers-Kerr,
B.Luo,
Y.Zhang,
M.Sollogoub,
Y.Bleriot,
C.Rovira,
G.J.Davies.
Analysis of the Reaction Coordinate of Alpha-L-Fucosidases: A Combined Structural and Quantum Mechanical Approach J.Am.Chem.Soc. V. 132 1804 2010.
ISSN: ISSN 0002-7863
PubMed: 20092273
DOI: 10.1021/JA908908Q
Page generated: Wed Jul 31 16:28:29 2024
|