Fluorine in PDB 3igu: Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate

All present enzymatic activity of Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate:
3.2.1.49;

The structure of Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate, PDB code: 3igu was solved by 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)	45.98 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.612, 113.649, 68.415, 90.00, 96.14, 90.00
R / Rfree (%)	16.4 / 19.9

The binding sites of Fluorine atom in the Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate (pdb code 3igu). 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 Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate, PDB code: 3igu:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate


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 Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:56.0 occ:1.00 F2A A:7JZ1001 0.0 56.0 1.0 C2 A:7JZ1001 1.3 39.4 1.0 F2B A:7JZ1001 2.1 38.5 1.0 C1 A:7JZ1001 2.3 40.3 1.0 C3 A:7JZ1001 2.3 32.5 1.0 O3 A:7JZ1001 2.5 24.2 1.0 O4 A:7JZ1001 2.8 23.7 1.0 OD2 A:ASP156 2.9 27.2 1.0 CE A:LYS154 3.1 17.8 1.0 C4 A:7JZ1001 3.1 22.8 1.0 NZ A:LYS154 3.3 17.4 1.0 CG A:ASP156 3.3 24.2 1.0 OD1 A:ASP156 3.5 22.6 1.0 O5 A:7JZ1001 3.5 33.3 1.0 NH1 A:ARG213 3.6 11.7 1.0 C5 A:7JZ1001 3.9 28.9 1.0 OG A:SER188 3.9 22.9 1.0 CB A:ASP156 4.4 21.4 1.0 CD A:LYS154 4.5 17.9 1.0 OD1 A:ASP217 4.6 18.5 1.0 CZ A:ARG213 4.7 15.1 1.0 CE1 A:TYR119 4.8 13.2 1.0 O A:HOH437 4.8 13.8 1.0 CB A:SER188 4.8 21.1 1.0 O A:HOH12 4.9 13.7 1.0 OH A:TYR192 4.9 28.0 1.0 C6 A:7JZ1001 4.9 23.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate


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 Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:38.5 occ:1.00 F2B A:7JZ1001 0.0 38.5 1.0 C2 A:7JZ1001 1.3 39.4 1.0 F2A A:7JZ1001 2.1 56.0 1.0 C3 A:7JZ1001 2.3 32.5 1.0 C1 A:7JZ1001 2.4 40.3 1.0 OD1 A:ASP217 2.7 18.5 1.0 O3 A:7JZ1001 3.0 24.2 1.0 O5 A:7JZ1001 3.1 33.3 1.0 O1 A:GOL1200 3.2 56.1 1.0 CG A:ASP217 3.4 19.2 1.0 OD2 A:ASP217 3.4 15.8 1.0 C4 A:7JZ1001 3.5 22.8 1.0 OD2 A:ASP156 3.6 27.2 1.0 NH1 A:ARG213 3.6 11.7 1.0 OD1 A:ASP156 3.8 22.6 1.0 C5 A:7JZ1001 3.8 28.9 1.0 OH A:TYR192 4.0 28.0 1.0 O4 A:7JZ1001 4.0 23.7 1.0 NH2 A:ARG213 4.1 12.2 1.0 CG A:ASP156 4.1 24.2 1.0 CZ A:ARG213 4.3 15.1 1.0 C1 A:GOL1200 4.3 58.1 1.0 O A:HOH12 4.4 13.7 1.0 O A:HOH608 4.8 28.4 1.0 O2 A:GOL1201 4.8 45.0 1.0 CB A:ASP217 4.8 17.9 1.0 CZ A:TYR192 4.9 25.6 1.0 O1 A:GOL1201 5.0 61.5 1.0 NZ A:LYS154 5.0 17.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate


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 Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:57.3 occ:1.00 F2A B:7JZ1001 0.0 57.3 1.0 C2 B:7JZ1001 1.3 53.2 1.0 F2B B:7JZ1001 2.1 53.1 1.0 C1 B:7JZ1001 2.3 52.6 1.0 C3 B:7JZ1001 2.4 46.2 1.0 O B:HOH723 2.6 25.7 1.0 O3 B:7JZ1001 2.6 39.7 1.0 OD2 B:ASP156 3.0 39.5 1.0 O4 B:7JZ1001 3.1 39.5 1.0 CE B:LYS154 3.2 26.0 1.0 C4 B:7JZ1001 3.3 44.3 1.0 NZ B:LYS154 3.3 23.9 1.0 NH1 B:ARG213 3.3 13.8 1.0 CG B:ASP156 3.4 30.5 1.0 OD1 B:ASP156 3.5 24.8 1.0 O5 B:7JZ1001 3.5 49.8 1.0 OG B:SER188 3.7 26.4 1.0 C5 B:7JZ1001 4.0 48.1 1.0 OD1 B:ASP217 4.4 22.7 1.0 CZ B:ARG213 4.4 12.9 1.0 CB B:ASP156 4.5 27.0 1.0 CD B:LYS154 4.7 25.9 1.0 CB B:SER188 4.7 22.0 1.0 O B:HOH438 4.9 22.2 1.0 NH2 B:ARG213 4.9 18.5 1.0 O B:HOH493 4.9 23.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate


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 Human Alpha-N-Acetylgalactosaminidase, Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:53.1 occ:1.00 F2B B:7JZ1001 0.0 53.1 1.0 C2 B:7JZ1001 1.3 53.2 1.0 F2A B:7JZ1001 2.1 57.3 1.0 C3 B:7JZ1001 2.3 46.2 1.0 C1 B:7JZ1001 2.4 52.6 1.0 OD1 B:ASP217 2.7 22.7 1.0 O B:HOH723 2.7 25.7 1.0 O5 B:7JZ1001 3.0 49.8 1.0 O3 B:7JZ1001 3.1 39.7 1.0 OD2 B:ASP217 3.3 26.4 1.0 O1 B:GOL1200 3.3 79.5 1.0 CG B:ASP217 3.3 22.4 1.0 C4 B:7JZ1001 3.5 44.3 1.0 OD2 B:ASP156 3.6 39.5 1.0 NH1 B:ARG213 3.6 13.8 1.0 C5 B:7JZ1001 3.8 48.1 1.0 OD1 B:ASP156 3.9 24.8 1.0 CG B:ASP156 4.1 30.5 1.0 NH2 B:ARG213 4.1 18.5 1.0 OH B:TYR192 4.1 35.4 1.0 O4 B:7JZ1001 4.2 39.5 1.0 CZ B:ARG213 4.3 12.9 1.0 O B:HOH438 4.4 22.2 1.0 C1 B:GOL1200 4.7 81.6 1.0 CB B:ASP217 4.8 20.1 1.0 O B:HOH637 4.8 41.4 1.0 CZ B:TYR192 5.0 29.4 1.0

N.E.Clark, S.C.Garman. The 1.9 A Structure of Human Alpha-N-Acetylgalactosaminidase: the Molecular Basis of Schindler and Kanzaki Diseases J.Mol.Biol. V. 393 435 2009.
ISSN: ISSN 0022-2836
PubMed: 19683538
DOI: 10.1016/J.JMB.2009.08.021