Chlorine in PDB 3vkk: Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex

All present enzymatic activity of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex:
3.2.1.21;

The structure of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex, PDB code: 3vkk was solved by J.Noguchi, Y.Hayashi, N.Okino, M.Ito, M.Kimura, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.69 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.733, 83.519, 90.892, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.2

The structure of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex (pdb code 3vkk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex, PDB code: 3vkk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl471 b:40.6 occ:1.00 OG A:SER77 2.6 18.4 1.0 O A:LEU78 2.6 22.3 1.0 OD2 A:ASP122 2.8 21.5 1.0 CB A:SER77 3.2 18.7 1.0 OD1 A:ASP122 3.2 20.4 1.0 O A:HOH503 3.2 23.9 1.0 N A:HIS120 3.4 20.0 1.0 CG A:ASP122 3.4 22.3 1.0 C A:LEU78 3.4 22.6 1.0 CB A:HIS120 3.5 19.6 1.0 O A:HOH509 3.5 22.1 1.0 N A:LEU78 3.8 21.7 1.0 CB A:ALA15 3.9 23.1 1.0 CA A:HIS120 4.0 20.2 1.0 O A:LEU118 4.0 20.4 1.0 C A:SER77 4.0 20.4 1.0 C A:TYR119 4.1 20.1 1.0 CA A:TYR119 4.1 20.0 1.0 N A:SER79 4.1 22.4 1.0 CA A:SER79 4.2 22.7 1.0 CA A:SER77 4.2 19.5 1.0 CA A:LEU78 4.3 21.3 1.0 O A:HIS120 4.4 20.7 1.0 N A:ALA15 4.5 22.2 1.0 C A:LEU118 4.5 20.8 1.0 N A:TYR119 4.5 19.8 1.0 C A:HIS120 4.6 19.9 1.0 O A:THR117 4.6 20.1 1.0 O A:SER77 4.7 19.4 1.0 CG A:HIS120 4.8 21.2 1.0 CA A:ALA15 4.8 22.3 1.0 CB A:ASP122 4.9 21.0 1.0 O A:HOH523 4.9 26.0 1.0 N A:TRP80 5.0 22.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Covalent Intermediate of Human Cytosolic Beta-Glucosidase-Mannose Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl473 b:60.3 occ:1.00 O A:HOH497 2.7 25.7 1.0 CZ A:PHE225 2.8 33.3 1.0 CE1 A:PHE225 2.8 36.2 1.0 NE2 A:GLN307 2.8 28.4 1.0 CE2 A:PHE225 3.2 35.5 1.0 CD1 A:PHE225 3.2 33.9 1.0 OE1 A:GLN307 3.3 34.9 1.0 CD A:GLN307 3.5 32.0 1.0 CG A:PHE225 3.5 30.5 1.0 CZ3 A:TRP345 3.5 35.6 1.0 CD2 A:PHE225 3.5 32.1 1.0 CH2 A:TRP345 3.6 35.6 1.0 O A:ALA226 4.0 24.7 1.0 CG2 A:VAL227 4.0 28.3 1.0 N A:TYR309 4.3 24.7 1.0 C A:ALA226 4.4 24.6 1.0 N A:ALA226 4.4 23.6 1.0 CB A:TYR309 4.5 27.2 1.0 CB A:PHE225 4.7 23.9 1.0 CD2 A:TYR309 4.7 30.6 1.0 N A:VAL227 4.8 25.9 1.0 CG A:TYR309 4.8 27.9 1.0 CE3 A:TRP345 4.9 36.7 1.0 CA A:PHE225 4.9 24.5 1.0 CZ2 A:TRP345 4.9 37.0 1.0 O A:GLN307 4.9 23.5 1.0 C A:PHE225 5.0 24.0 1.0 CG A:GLN307 5.0 25.2 1.0 C A:TYR308 5.0 23.7 1.0 CA A:TYR309 5.0 25.8 1.0 CA A:VAL227 5.0 26.4 1.0

J.Noguchi, Y.Hayashi, N.Okino, M.Ito, M.Kimura, Y.Kakuta. Structural Basis For Inhibition Mechanism of Human Cytosolic Beta-Glucosidase By Monnoside To Be Published.