Fluorine in PDB 3hg4: Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate

All present enzymatic activity of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate:
3.2.1.22;

The structure of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate, PDB code: 3hg4 was solved by A.I.Guce, N.E.Clark, S.C.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.05 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.218, 90.218, 216.615, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 22.1

The binding sites of Fluorine atom in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate (pdb code 3hg4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate, PDB code: 3hg4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:44.1 occ:1.00 F2A A:7JZ801 0.0 44.1 1.0 C2 A:7JZ801 1.3 44.4 1.0 F2B A:7JZ801 2.2 43.5 1.0 C1 A:7JZ801 2.3 45.2 1.0 C3 A:7JZ801 2.3 44.1 1.0 O3 A:7JZ801 2.6 42.1 1.0 OD2 A:ASP170 2.8 47.9 1.0 O4 A:7JZ801 3.0 45.3 1.0 CG A:ASP170 3.1 47.0 1.0 C4 A:7JZ801 3.1 44.8 1.0 CE A:LYS168 3.2 42.8 1.0 OD1 A:ASP170 3.3 46.9 1.0 NZ A:LYS168 3.3 42.7 1.0 O5 A:7JZ801 3.5 44.5 1.0 CG A:GLU203 3.5 50.9 1.0 OE1 A:GLU203 3.6 55.9 1.0 CD A:GLU203 3.7 54.0 1.0 NH1 A:ARG227 3.7 43.1 1.0 C5 A:7JZ801 3.9 44.4 1.0 CB A:ASP170 4.2 46.6 1.0 OE2 A:GLU203 4.5 55.9 1.0 CD A:LYS168 4.6 44.0 1.0 CE1 A:TYR134 4.6 43.9 1.0 OD1 A:ASP231 4.7 50.0 1.0 O A:HOH1012 4.8 26.6 1.0 CZ A:ARG227 4.8 44.4 1.0 C6 A:7JZ801 4.8 44.0 1.0 CB A:GLU203 4.8 49.4 1.0 CA A:ASP170 4.8 46.4 1.0 O A:HOH1457 4.9 43.7 1.0

Fluorine binding site 2 out of 4 in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:43.5 occ:1.00 F2B A:7JZ801 0.0 43.5 1.0 C2 A:7JZ801 1.3 44.4 1.0 F2A A:7JZ801 2.2 44.1 1.0 C3 A:7JZ801 2.3 44.1 1.0 C1 A:7JZ801 2.4 45.2 1.0 O A:HOH1457 2.8 43.7 1.0 O3 A:7JZ801 3.0 42.1 1.0 OD1 A:ASP231 3.1 50.0 1.0 O5 A:7JZ801 3.2 44.5 1.0 OD1 A:ASP170 3.3 46.9 1.0 OD2 A:ASP170 3.4 47.9 1.0 OH A:TYR207 3.5 52.9 1.0 C4 A:7JZ801 3.6 44.8 1.0 CG A:ASP170 3.7 47.0 1.0 NH1 A:ARG227 3.8 43.1 1.0 CG A:ASP231 3.9 48.1 1.0 C5 A:7JZ801 4.0 44.4 1.0 OD2 A:ASP231 4.0 49.7 1.0 CG A:GLU203 4.2 50.9 1.0 NH2 A:ARG227 4.2 44.5 1.0 CD2 A:LEU206 4.2 49.7 1.0 O4 A:7JZ801 4.3 45.3 1.0 CE2 A:TYR207 4.3 52.5 1.0 CZ A:ARG227 4.4 44.4 1.0 CZ A:TYR207 4.4 52.5 1.0 CD A:GLU203 5.0 54.0 1.0 O A:HOH1019 5.0 27.0 1.0

Fluorine binding site 3 out of 4 in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:50.6 occ:1.00 F2A B:7JZ802 0.0 50.6 1.0 C2 B:7JZ802 1.3 50.4 1.0 F2B B:7JZ802 2.2 49.9 1.0 C1 B:7JZ802 2.3 49.8 1.0 C3 B:7JZ802 2.4 50.0 1.0 O3 B:7JZ802 2.7 49.4 1.0 OD2 B:ASP170 2.7 48.6 1.0 O4 B:7JZ802 3.0 50.6 1.0 CG B:ASP170 3.1 47.3 1.0 C4 B:7JZ802 3.2 49.7 1.0 CE B:LYS168 3.2 43.7 1.0 OD1 B:ASP170 3.3 47.5 1.0 CG B:GLU203 3.4 51.7 1.0 NZ B:LYS168 3.4 43.3 1.0 O5 B:7JZ802 3.5 49.7 1.0 CD B:GLU203 3.5 55.1 1.0 OE2 B:GLU203 3.6 56.5 1.0 NH1 B:ARG227 3.8 44.8 1.0 C5 B:7JZ802 3.9 49.3 1.0 CB B:ASP170 4.2 46.6 1.0 OE1 B:GLU203 4.2 56.6 1.0 CE1 B:TYR134 4.6 43.9 1.0 CD B:LYS168 4.6 44.1 1.0 CB B:GLU203 4.6 49.7 1.0 O B:HOH1010 4.8 28.5 1.0 CZ B:ARG227 4.8 45.5 1.0 C6 B:7JZ802 4.8 48.1 1.0 OD1 B:ASP231 4.8 50.4 1.0 CA B:ASP170 4.9 46.5 1.0

Fluorine binding site 4 out of 4 in the Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Alpha-Galactosidase Catalytic Mechanism 3. Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:49.9 occ:1.00 F2B B:7JZ802 0.0 49.9 1.0 C2 B:7JZ802 1.3 50.4 1.0 F2A B:7JZ802 2.2 50.6 1.0 C1 B:7JZ802 2.3 49.8 1.0 C3 B:7JZ802 2.3 50.0 1.0 O B:HOH1350 3.0 47.7 1.0 O3 B:7JZ802 3.1 49.4 1.0 OD1 B:ASP231 3.1 50.4 1.0 O5 B:7JZ802 3.1 49.7 1.0 OD2 B:ASP170 3.3 48.6 1.0 OD1 B:ASP170 3.4 47.5 1.0 OH B:TYR207 3.6 52.5 1.0 C4 B:7JZ802 3.6 49.7 1.0 CG B:ASP170 3.7 47.3 1.0 NH1 B:ARG227 3.9 44.8 1.0 CG B:ASP231 3.9 47.9 1.0 OD2 B:ASP231 3.9 48.6 1.0 C5 B:7JZ802 3.9 49.3 1.0 NH2 B:ARG227 4.0 45.4 1.0 CG B:GLU203 4.1 51.7 1.0 O4 B:7JZ802 4.3 50.6 1.0 CZ B:ARG227 4.3 45.5 1.0 CE2 B:TYR207 4.3 52.2 1.0 CD2 B:LEU206 4.4 50.0 1.0 CZ B:TYR207 4.4 52.1 1.0 CD B:GLU203 4.9 55.1 1.0 O B:HOH1124 5.0 32.0 1.0

A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, S.C.Garman. Catalytic Mechanism of Human Alpha-Galactosidase. J.Biol.Chem. V. 285 3625 2010.
ISSN: ISSN 0021-9258
PubMed: 19940122
DOI: 10.1074/JBC.M109.060145