Sodium in PDB 6moz: Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor

All present enzymatic activity of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor:
3.2.1.45;

The structure of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor, PDB code: 6moz was solved by A.C.Patterson-Orazem, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.280, 285.010, 91.680, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.8

The structure of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Sodium atom in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor (pdb code 6moz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 32 binding sites of Sodium where determined in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor, PDB code: 6moz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:36.0 occ:1.00 OD1 A:ASP153 2.5 35.0 1.0 NZ A:LYS157 2.8 32.2 1.0 OH A:TYR133 2.8 31.4 1.0 OD2 A:ASP153 3.1 43.4 1.0 CG A:ASP153 3.1 35.2 1.0 OH A:TYR135 3.2 38.6 1.0 CA A:ALA124 3.4 33.0 1.0 O A:HOH637 3.4 31.1 1.0 N A:ALA124 3.6 35.0 1.0 CE1 A:TYR133 3.6 27.9 1.0 CZ A:TYR133 3.6 33.3 1.0 C A:ALA124 3.8 32.4 1.0 CE1 A:TYR135 3.8 39.9 1.0 O A:ALA124 3.9 35.0 1.0 CZ A:TYR135 3.9 40.4 1.0 CE A:LYS157 3.9 33.8 1.0 CD A:LYS157 4.1 34.0 1.0 OD2 A:ASP87 4.1 37.3 1.0 CB A:GLU152 4.2 26.1 1.0 O A:PRO122 4.3 31.5 1.0 CB A:ASP153 4.5 40.0 1.0 N A:ASP153 4.5 32.6 1.0 CB A:ALA124 4.6 30.3 1.0 N A:SER125 4.7 30.8 1.0 OD1 A:ASP87 4.7 37.2 1.0 CG A:PRO150 4.8 29.0 1.0 C A:MET123 4.8 36.5 1.0 CG A:ASP87 4.9 37.0 1.0 CA A:ASP153 4.9 35.1 1.0 CD1 A:TYR133 4.9 38.0 1.0 C A:GLU152 4.9 40.5 1.0 CD A:PRO150 4.9 32.4 1.0 CE2 A:TYR133 5.0 32.6 1.0

Sodium binding site 2 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:40.7 occ:1.00 O A:GLN226 2.8 41.3 1.0 N A:LEU174 2.8 41.7 1.0 O A:HOH658 2.9 47.9 1.0 N A:TRP228 3.2 33.3 1.0 CA A:SER173 3.5 35.8 1.0 C A:SER173 3.6 36.9 1.0 C A:PHE227 3.7 38.0 1.0 CB A:LEU174 3.7 33.9 1.0 CA A:LEU174 3.7 38.8 1.0 O A:VAL172 3.7 38.2 1.0 CA A:PHE227 3.8 34.6 1.0 CG A:LEU174 3.8 38.7 1.0 C A:GLN226 3.8 37.0 1.0 CB A:TRP228 4.0 37.5 1.0 O A:LEU174 4.1 33.3 1.0 CA A:TRP228 4.1 33.2 1.0 N A:PHE227 4.2 35.9 1.0 CB A:SER173 4.3 27.8 1.0 C A:LEU174 4.4 33.5 1.0 N A:SER173 4.5 34.3 1.0 C A:VAL172 4.5 38.6 1.0 O A:PHE227 4.5 36.2 1.0 CD1 A:LEU174 4.5 33.8 1.0 OG A:SER173 4.7 33.8 1.0 O A:HOH655 4.7 34.3 1.0 O A:SER173 4.8 37.2 1.0 CD2 A:LEU174 4.9 37.0 1.0

Sodium binding site 3 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:42.5 occ:1.00 OG A:SER484 2.5 41.8 1.0 OG A:SER488 2.8 38.9 1.0 O A:VAL460 2.9 37.5 1.0 CB A:SER484 3.5 42.4 1.0 CG A:HIS490 3.5 35.8 1.0 N A:HIS490 3.5 35.7 1.0 CD2 A:HIS490 3.6 39.4 1.0 O A:SER488 3.7 34.5 1.0 C A:VAL460 3.8 38.4 1.0 CB A:HIS490 3.8 35.2 1.0 CG1 A:VAL460 3.8 36.3 1.0 C A:SER488 3.8 36.6 1.0 CA A:ILE489 3.8 37.0 1.0 CA A:SER484 3.9 38.3 1.0 ND1 A:HIS490 3.9 39.1 1.0 C A:ILE489 3.9 37.6 1.0 N A:ILE489 4.0 37.1 1.0 CB A:SER488 4.0 36.6 1.0 NE2 A:HIS490 4.1 40.2 1.0 N A:ASN462 4.1 33.1 1.0 CE1 A:HIS490 4.2 40.4 1.0 CB A:VAL460 4.2 35.3 1.0 CA A:HIS490 4.3 39.9 1.0 CB A:ASN462 4.3 32.1 1.0 N A:LEU461 4.5 34.1 1.0 CA A:LEU461 4.5 36.5 1.0 C A:LEU461 4.5 31.8 1.0 C A:SER484 4.5 37.5 1.0 CA A:SER488 4.6 34.7 1.0 CD A:PRO485 4.6 36.4 1.0 CA A:VAL460 4.7 33.6 1.0 N A:PRO485 4.7 37.2 1.0 O A:PRO485 4.8 41.9 1.0 O A:ILE489 4.8 33.3 1.0 CA A:ASN462 4.9 39.3 1.0

Sodium binding site 4 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:46.2 occ:1.00 N A:TYR11 2.8 42.6 1.0 O A:SER13 2.8 41.2 1.0 N A:PHE9 2.9 41.7 1.0 O A:LEU354 3.0 35.9 1.0 N A:GLY10 3.3 44.7 1.0 CA A:TYR11 3.4 40.2 1.0 CB A:TYR11 3.4 41.8 1.0 C A:PHE9 3.5 43.9 1.0 O A:TYR11 3.6 41.3 1.0 C A:TYR11 3.6 41.3 1.0 CA A:PHE9 3.6 42.6 1.0 OG A:SER8 3.7 39.0 1.0 C A:GLY10 3.8 44.7 1.0 C A:SER8 3.9 43.7 1.0 CA A:SER8 3.9 37.8 1.0 CA A:GLY355 4.0 37.7 1.0 CB A:PHE9 4.0 37.9 1.0 C A:SER13 4.0 39.5 1.0 CA A:GLY10 4.1 41.4 1.0 C A:LEU354 4.1 40.0 1.0 CD2 A:TYR11 4.1 40.3 1.0 CG A:TYR11 4.2 46.6 1.0 O A:PHE9 4.3 41.1 1.0 CB A:SER8 4.3 42.1 1.0 N A:SER13 4.4 39.8 1.0 N A:SER12 4.4 38.3 1.0 C A:GLY355 4.4 38.0 1.0 O A:GLY355 4.5 37.0 1.0 N A:GLY355 4.5 38.8 1.0 CA A:SER13 4.9 39.5 1.0 CA A:VAL14 4.9 35.3 1.0 N A:VAL14 4.9 33.4 1.0 O A:GLY10 4.9 47.8 1.0

Sodium binding site 5 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:55.6 occ:1.00 O A:ASP443 2.7 48.9 1.0 N A:ARG463 2.8 40.9 1.0 OD2 A:ASP445 3.0 53.7 1.0 CB A:ARG463 3.1 41.4 1.0 CD A:ARG463 3.4 53.6 1.0 CA A:ARG463 3.5 44.5 1.0 O A:LEU461 3.5 40.5 1.0 CG A:ARG463 3.6 44.3 1.0 NH1 A:ARG463 3.6 68.4 1.0 C A:ASP443 3.8 47.1 1.0 C A:ASN462 3.8 43.9 1.0 CA A:LEU444 3.9 39.9 1.0 CG A:ASP445 3.9 49.4 1.0 N A:ASP445 3.9 34.6 1.0 CA A:ASN462 4.0 39.3 1.0 C A:LEU444 4.1 39.9 1.0 NE A:ARG463 4.1 55.9 1.0 CZ A:ARG463 4.2 65.5 1.0 C A:LEU461 4.3 31.8 1.0 C A:ARG463 4.3 39.7 1.0 N A:LEU444 4.3 43.4 1.0 N A:SER464 4.4 39.4 1.0 OD1 A:ASP445 4.5 46.0 1.0 N A:ASN462 4.5 33.1 1.0 OD1 A:ASN462 4.6 41.2 1.0 CB A:ASP445 4.7 41.7 1.0 O A:LEU444 4.8 41.7 1.0 CG A:LEU461 4.8 36.0 1.0 CA A:ASP445 4.9 36.6 1.0 O A:ASN462 5.0 44.9 1.0

Sodium binding site 6 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:44.5 occ:1.00 OG1 A:THR68 2.5 38.4 1.0 O A:VAL437 2.9 35.5 1.0 CB A:THR68 3.2 36.0 1.0 O A:LEU66 3.3 35.0 1.0 N A:THR68 3.4 41.5 1.0 CG A:LEU66 3.7 41.1 1.0 N A:SER439 3.7 38.4 1.0 CB A:SER439 3.8 43.3 1.0 CD2 A:LEU66 3.8 40.7 1.0 C A:LEU66 3.8 37.4 1.0 C A:VAL437 3.8 36.5 1.0 CA A:THR68 3.9 34.6 1.0 CA A:SER439 4.0 37.4 1.0 C A:LEU67 4.1 39.8 1.0 CA A:LEU67 4.2 31.4 1.0 C A:ALA438 4.2 42.4 1.0 CB A:LEU66 4.2 34.9 1.0 N A:LEU67 4.2 33.2 1.0 CG1 A:VAL437 4.4 42.1 1.0 CB A:VAL437 4.4 38.2 1.0 CG2 A:THR68 4.4 36.2 1.0 CA A:ALA438 4.6 32.5 1.0 N A:ALA438 4.6 34.1 1.0 CA A:LEU66 4.6 32.4 1.0 CA A:VAL437 4.7 38.2 1.0 O A:ALA438 4.8 37.2 1.0 OG A:SER439 4.9 37.6 1.0 O A:LEU67 5.0 36.0 1.0

Sodium binding site 7 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:42.7 occ:1.00 OH A:TYR212 2.7 39.1 1.0 O A:THR180 2.8 32.3 1.0 O A:MET123 3.0 35.7 1.0 CE1 A:TYR212 3.2 36.6 1.0 CZ A:TYR212 3.2 36.0 1.0 NA A:NA515 3.5 40.6 1.0 CB A:ALA124 3.6 30.3 1.0 CH2 A:TRP209 3.8 29.0 1.0 C A:MET123 3.9 36.5 1.0 C A:THR180 4.0 37.9 1.0 CZ3 A:TRP209 4.3 28.1 1.0 CB A:PRO178 4.4 27.8 1.0 CB A:MET123 4.4 29.0 1.0 CE2 A:TYR212 4.4 41.3 1.0 CB A:THR134 4.4 35.9 1.0 CD1 A:TYR212 4.4 31.5 1.0 N A:ALA124 4.6 35.0 1.0 CG2 A:THR134 4.7 29.4 1.0 CA A:SER181 4.7 27.9 1.0 CA A:ALA124 4.7 33.0 1.0 N A:THR180 4.7 33.1 1.0 CD2 A:TYR135 4.8 36.7 1.0 N A:SER181 4.8 32.1 1.0 CA A:MET123 4.8 35.3 1.0 CA A:THR134 4.8 34.1 1.0 CZ2 A:TRP209 4.9 27.8 1.0 CA A:PRO178 4.9 26.5 1.0 CE2 A:TYR135 4.9 36.3 1.0 CA A:THR180 5.0 33.0 1.0

Sodium binding site 8 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:46.5 occ:1.00 N A:LEU314 2.7 53.3 1.0 O A:HIS311 2.8 32.0 1.0 OD1 A:ASP315 3.0 43.0 1.0 C A:LEU314 3.1 54.9 1.0 N A:ARG285 3.2 33.7 1.0 CA A:LEU314 3.2 51.9 1.0 N A:ASP315 3.2 46.2 1.0 CB A:LEU314 3.3 51.0 1.0 C A:TRP312 3.5 37.7 1.0 CA A:GLN284 3.5 32.5 1.0 CB A:GLN284 3.5 35.3 1.0 OE1 A:GLN284 3.5 47.7 1.0 N A:TYR313 3.6 43.4 1.0 O A:TRP312 3.7 34.6 1.0 O A:LEU314 3.8 60.5 1.0 C A:GLN284 3.8 33.3 1.0 C A:HIS311 3.8 29.7 1.0 CG A:ARG285 3.9 40.4 1.0 CA A:TRP312 3.9 35.4 1.0 C A:TYR313 3.9 50.5 1.0 CA A:ASP315 4.0 52.6 1.0 CG A:ASP315 4.1 49.7 1.0 CA A:ARG285 4.2 40.1 1.0 N A:TRP312 4.2 27.7 1.0 CB A:ARG285 4.3 41.9 1.0 CA A:TYR313 4.3 47.8 1.0 CG A:LEU314 4.4 49.2 1.0 N A:LEU286 4.4 43.4 1.0 CD A:GLN284 4.4 45.8 1.0 CG A:GLN284 4.5 40.4 1.0 CB A:ASP315 4.6 51.9 1.0 CD A:ARG285 4.7 41.3 1.0 N A:GLN284 4.8 32.2 1.0 C A:ARG285 4.8 39.2 1.0 O A:GLN284 4.9 34.2 1.0 O A:TYR313 5.0 51.2 1.0 OD2 A:ASP315 5.0 45.3 1.0

Sodium binding site 9 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:42.2 occ:1.00 O A:HOH622 2.4 28.6 1.0 O A:ASP399 2.9 38.9 1.0 ND2 A:ASN382 3.0 34.2 1.0 N A:ASN382 3.2 24.1 1.0 CB A:ASN382 3.3 24.1 1.0 CG2 A:VAL398 3.4 36.9 1.0 CD1 A:TRP381 3.6 35.7 1.0 CG A:ASN382 3.7 28.2 1.0 CB A:CYS342 3.7 45.0 1.0 CA A:ASN382 3.8 27.4 1.0 CB A:TRP381 3.8 32.1 1.0 CD1 A:LEU385 3.8 26.9 1.0 O A:ASN382 3.8 31.3 1.0 CG A:TRP381 3.9 33.8 1.0 C A:ASP399 4.0 35.9 1.0 C A:TRP381 4.1 29.6 1.0 CB A:SER400 4.1 33.5 1.0 C A:ASN382 4.3 29.0 1.0 CA A:SER400 4.3 34.1 1.0 SG A:CYS342 4.5 48.3 1.0 CA A:TRP381 4.5 27.7 1.0 NE1 A:TRP381 4.5 35.4 1.0 CG A:LEU385 4.6 33.0 1.0 N A:SER400 4.6 37.3 1.0 O A:HOH618 4.6 36.9 1.0 OG A:SER400 4.6 32.8 1.0 CB A:VAL398 4.8 41.4 1.0 OD1 A:ASN382 4.9 28.0 1.0 CA A:CYS342 4.9 44.1 1.0 N A:ASP399 5.0 38.2 1.0

Sodium binding site 10 out of 32 in the Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Acid-Beta-Glucosidase in Complex with An Aromatic Pyrrolidine Iminosugar Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:39.6 occ:1.00 OG1 A:THR132 2.7 31.2 1.0 O A:HOH621 2.9 28.9 1.0 N A:THR132 3.3 39.6 1.0 CB A:THR132 3.7 35.4 1.0 CG2 A:THR132 3.8 28.2 1.0 CA A:THR132 4.0 37.1 1.0 O A:THR132 4.2 62.6 1.0 CA A:ARG131 4.2 36.0 1.0 C A:ARG131 4.3 39.6 1.0 CB A:ARG131 4.4 34.3 1.0 C A:THR132 4.6 44.3 1.0

M.Martinez-Bailen, A.T.Carmona, A.C.Patterson-Orazem, R.L.Lieberman, D.Ide, M.Kubo, A.Kato, I.Robina, A.J.Moreno-Vargas. Exploring Substituent Diversity on Pyrrolidine-Aryltriazole Iminosugars: Structural Basis of Beta-Glucocerebrosidase Inhibition. Bioorg.Chem. V. 86 652 2019.
ISSN: ISSN 0045-2068
PubMed: 30825709
DOI: 10.1016/J.BIOORG.2019.02.025