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Fluorine in PDB 1hl9: Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor

Enzymatic activity of Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor:
3.2.1.51;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor, PDB code: 1hl9 was solved by G.Sulzenbacher, C.Bignon, Y.Bourne, B.Henrissat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 172.157, 172.157, 167.331, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor (pdb code 1hl9). 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 Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor, PDB code: 1hl9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1hl9

Go back to Fluorine Binding Sites List in 1hl9
Fluorine binding site 1 out of 4 in the Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor


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 Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1449

b:36.5
occ:0.60
 F2 A:FUF1449 0.0 36.5 0.6
F2 A:FUF1449 1.0 36.2 0.4
C2 A:FUF1449 1.4 36.7 0.6
C2 A:FUF1449 1.9 36.0 0.4
C3 A:FUF1449 2.2 36.7 0.4
C1 A:FUF1449 2.4 36.7 0.6
C3 A:FUF1449 2.5 36.9 0.6
C1 A:FUF1449 2.7 35.6 0.4
O3 A:FUF1449 2.8 36.4 0.4
O1 A:FUF1449 2.9 36.7 0.6
O3 A:FUF1449 2.9 36.5 0.6
NE1 A:TRP67 3.2 29.8 1.0
NE2 A:HIS129 3.3 24.7 1.0
O5 A:FUF1449 3.5 36.4 0.4
CZ2 A:TRP67 3.6 29.8 1.0
O5 A:FUF1449 3.7 36.8 0.6
C4 A:FUF1449 3.7 36.9 0.4
CE2 A:TRP67 3.7 30.4 1.0
C4 A:FUF1449 3.8 37.1 0.6
OD1 A:ASP224 3.9 33.1 1.0
C5 A:FUF1449 4.0 37.0 0.4
CE1 A:HIS129 4.1 25.1 1.0
C5 A:FUF1449 4.2 37.5 0.6
CD2 A:HIS129 4.3 25.7 1.0
O4 A:FUF1449 4.3 35.9 0.6
O4 A:FUF1449 4.4 36.0 0.4
CD1 A:TRP67 4.4 30.2 1.0
CE A:MET225 4.5 40.9 1.0
SD A:MET225 4.6 39.6 1.0
CG A:MET225 4.9 33.1 1.0
CH2 A:TRP67 4.9 31.2 1.0
CD2 A:TYR64 4.9 51.3 1.0
CG A:ASP224 5.0 28.8 1.0

Fluorine binding site 2 out of 4 in 1hl9

Go back to Fluorine Binding Sites List in 1hl9
Fluorine binding site 2 out of 4 in the Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor


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 Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1449

b:36.2
occ:0.40
 F2 A:FUF1449 0.0 36.2 0.4
F2 A:FUF1449 1.0 36.5 0.6
C2 A:FUF1449 1.4 36.0 0.4
C2 A:FUF1449 1.6 36.7 0.6
NE2 A:HIS129 2.4 24.7 1.0
C3 A:FUF1449 2.4 36.7 0.4
C1 A:FUF1449 2.4 35.6 0.4
C3 A:FUF1449 2.7 36.9 0.6
C1 A:FUF1449 2.8 36.7 0.6
O3 A:FUF1449 2.9 36.4 0.4
O3 A:FUF1449 2.9 36.5 0.6
O1 A:FUF1449 3.0 36.7 0.6
CE1 A:HIS129 3.1 25.1 1.0
NE1 A:TRP67 3.3 29.8 1.0
OD1 A:ASP224 3.4 33.1 1.0
CD2 A:HIS129 3.5 25.7 1.0
CZ2 A:TRP67 3.6 29.8 1.0
O5 A:FUF1449 3.6 36.4 0.4
C4 A:FUF1449 3.7 36.9 0.4
CE2 A:TRP67 3.7 30.4 1.0
O5 A:FUF1449 3.8 36.8 0.6
C4 A:FUF1449 3.9 37.1 0.6
O4 A:FUF1449 4.1 35.9 0.6
O4 A:FUF1449 4.1 36.0 0.4
C5 A:FUF1449 4.1 37.0 0.4
CE A:MET225 4.2 40.9 1.0
CG A:MET225 4.3 33.1 1.0
SD A:MET225 4.3 39.6 1.0
ND1 A:HIS129 4.3 26.9 1.0
CE1 A:HIS128 4.4 30.3 1.0
CG A:ASP224 4.5 28.8 1.0
C5 A:FUF1449 4.5 37.5 0.6
NE2 A:HIS128 4.5 28.6 1.0
CD1 A:TRP67 4.5 30.2 1.0
CG A:HIS129 4.5 25.6 1.0
OH A:TYR171 4.7 24.7 1.0
CH2 A:TRP67 4.8 31.2 1.0
OD2 A:ASP224 4.8 27.2 1.0

Fluorine binding site 3 out of 4 in 1hl9

Go back to Fluorine Binding Sites List in 1hl9
Fluorine binding site 3 out of 4 in the Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor


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 Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1449

b:37.6
occ:0.40
 F2 B:FUF1449 0.0 37.6 0.4
F2 B:FUF1449 0.7 37.2 0.6
C2 B:FUF1449 1.4 37.9 0.4
C2 B:FUF1449 1.7 37.5 0.6
C3 B:FUF1449 2.2 38.6 0.6
C1 B:FUF1449 2.4 38.1 0.4
C3 B:FUF1449 2.4 38.6 0.4
C1 B:FUF1449 2.6 36.9 0.6
O1 B:FUF1449 2.8 37.9 0.4
O3 B:FUF1449 2.9 38.0 0.6
O3 B:FUF1449 2.9 38.1 0.4
NE1 B:TRP67 3.2 38.6 1.0
NE2 B:HIS129 3.4 33.3 1.0
O5 B:FUF1449 3.4 38.2 0.6
CZ2 B:TRP67 3.5 38.1 1.0
C4 B:FUF1449 3.6 39.0 0.6
O5 B:FUF1449 3.6 38.7 0.4
CE2 B:TRP67 3.7 38.9 1.0
C4 B:FUF1449 3.8 38.9 0.4
OD1 B:ASP224 3.9 40.4 1.0
C5 B:FUF1449 4.0 38.9 0.6
C5 B:FUF1449 4.2 39.0 0.4
CE1 B:HIS129 4.3 33.9 1.0
O4 B:FUF1449 4.3 39.7 0.4
CD2 B:HIS129 4.3 35.8 1.0
O4 B:FUF1449 4.3 40.0 0.6
SD B:MET225 4.4 43.8 1.0
CD1 B:TRP67 4.4 39.4 1.0
CG B:MET225 4.7 39.4 1.0
CD1 B:TYR64 4.7 54.5 1.0
CE B:MET225 4.7 45.9 1.0
O B:HOH2014 4.7 59.3 1.0
CE1 B:TYR64 4.8 54.8 1.0
CH2 B:TRP67 4.8 38.9 1.0
CG B:ASP224 4.9 33.1 1.0

Fluorine binding site 4 out of 4 in 1hl9

Go back to Fluorine Binding Sites List in 1hl9
Fluorine binding site 4 out of 4 in the Crystal Structure of Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor


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 Thermotoga Maritima Alpha-Fucosidase in Complex with A Mechanism Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1449

b:37.2
occ:0.60
 F2 B:FUF1449 0.0 37.2 0.6
F2 B:FUF1449 0.7 37.6 0.4
C2 B:FUF1449 1.4 37.5 0.6
C2 B:FUF1449 1.5 37.9 0.4
C3 B:FUF1449 2.4 38.6 0.6
C1 B:FUF1449 2.4 36.9 0.6
C3 B:FUF1449 2.7 38.6 0.4
C1 B:FUF1449 2.7 38.1 0.4
NE2 B:HIS129 2.7 33.3 1.0
O3 B:FUF1449 2.9 38.1 0.4
O3 B:FUF1449 2.9 38.0 0.6
O1 B:FUF1449 2.9 37.9 0.4
NE1 B:TRP67 3.3 38.6 1.0
CZ2 B:TRP67 3.5 38.1 1.0
OD1 B:ASP224 3.5 40.4 1.0
O5 B:FUF1449 3.5 38.2 0.6
CE1 B:HIS129 3.5 33.9 1.0
CE2 B:TRP67 3.7 38.9 1.0
C4 B:FUF1449 3.7 39.0 0.6
CD2 B:HIS129 3.7 35.8 1.0
O5 B:FUF1449 3.8 38.7 0.4
C4 B:FUF1449 3.9 38.9 0.4
SD B:MET225 4.1 43.8 1.0
C5 B:FUF1449 4.1 38.9 0.6
O4 B:FUF1449 4.1 39.7 0.4
CG B:MET225 4.1 39.4 1.0
O4 B:FUF1449 4.2 40.0 0.6
C5 B:FUF1449 4.4 39.0 0.4
CE B:MET225 4.5 45.9 1.0
CG B:ASP224 4.5 33.1 1.0
CD1 B:TRP67 4.5 39.4 1.0
CE1 B:HIS128 4.6 33.8 1.0
ND1 B:HIS129 4.7 34.2 1.0
CH2 B:TRP67 4.7 38.9 1.0
OD2 B:ASP224 4.8 34.4 1.0
CG B:HIS129 4.9 33.9 1.0
NE2 B:HIS128 4.9 31.7 1.0

Reference:

G.Sulzenbacher, C.Bignon, T.Nishimura, C.A.Tarling, S.G.Withers, B.Henrissat, Y.Bourne. Crystal Structure of Thermotoga Maritima {Alpha}-L-Fucosidase: Insights Into the Catalytic Mechanism and the Molecular Basis For Fucosidosis J.Biol.Chem. V. 279 13119 2004.
ISSN: ISSN 0021-9258
PubMed: 14715651
DOI: 10.1074/JBC.M313783200
Page generated: Wed Jul 31 11:31:12 2024

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