Sodium in PDB 3vsb: Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex

All present enzymatic activity of Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex:
3.4.21.62;

The structure of Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 3vsb was solved by V.S.Stoll, B.T.Eger, R.C.Hynes, V.Martichonok, J.B.Jones, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.000, 55.400, 76.600, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 29.9

The binding sites of Sodium atom in the Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex (pdb code 3vsb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 3vsb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:10.0 occ:1.00 O A:TYR171 1.9 24.4 1.0 O A:ALA169 1.9 5.6 1.0 O A:VAL174 2.1 2.0 1.0 C A:TYR171 3.1 2.0 1.0 C A:ALA169 3.1 5.7 1.0 C A:VAL174 3.2 28.7 1.0 C A:LYS170 3.7 2.0 1.0 N A:TYR171 3.7 2.0 1.0 O A:LYS170 3.9 10.7 1.0 CA A:VAL174 4.0 28.7 1.0 CA A:TYR171 4.0 2.0 1.0 CB A:VAL174 4.0 2.0 1.0 N A:ASP172 4.0 8.7 1.0 N A:LYS170 4.1 2.0 1.0 CA A:ALA169 4.1 5.7 1.0 N A:VAL174 4.1 28.7 1.0 N A:ALA176 4.2 2.0 1.0 CA A:ASP172 4.2 8.7 1.0 N A:ILE175 4.2 7.4 1.0 CA A:LYS170 4.2 2.0 1.0 CB A:ALA176 4.4 7.8 1.0 C A:ILE175 4.5 7.4 1.0 CA A:ILE175 4.5 7.4 1.0 C A:ASP172 4.5 8.7 1.0 CG1 A:VAL174 4.6 2.0 1.0 OE1 A:GLU197 4.6 13.8 1.0 NH2 A:ARG247 4.7 7.2 1.0 O A:PRO168 4.7 11.1 1.0 CA A:ALA176 4.8 2.0 1.0 CB A:TYR171 4.8 24.4 1.0 CB A:ALA169 4.9 5.6 1.0 O A:ASP172 4.9 26.5 1.0 CB A:GLU195 4.9 7.4 1.0 O A:GLU195 4.9 7.4 1.0

Sodium binding site 2 out of 2 in the Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Subtilisin Carlsberg D-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:10.0 occ:1.00 O A:VAL81 1.9 4.0 1.0 OD1 A:ASP41 2.0 9.9 1.0 OD2 A:ASP41 2.2 9.9 1.0 NE2 A:GLN2 2.2 5.6 1.0 O A:LEU75 2.2 2.8 1.0 OD1 A:ASN77 2.3 14.4 1.0 CG A:ASP41 2.4 9.9 1.0 O A:THR79 2.6 20.9 1.0 C A:VAL81 3.1 2.0 1.0 CG A:ASN77 3.3 14.4 1.0 CD A:GLN2 3.4 5.6 1.0 C A:LEU75 3.4 6.1 1.0 N A:VAL81 3.6 2.0 1.0 C A:THR79 3.8 15.8 1.0 CG A:GLN2 3.8 5.6 1.0 ND2 A:ASN77 3.9 14.4 1.0 CB A:ASP41 4.0 9.9 1.0 CA A:VAL81 4.0 2.0 1.0 N A:ASN77 4.0 25.6 1.0 C A:GLY80 4.1 14.7 1.0 N A:LEU75 4.2 6.1 1.0 CA A:LEU75 4.2 6.1 1.0 N A:LEU82 4.2 2.0 1.0 OE1 A:GLN2 4.4 5.6 1.0 CA A:GLY80 4.4 14.7 1.0 C A:ALA74 4.4 11.6 1.0 N A:ASP76 4.5 10.0 1.0 CA A:LEU82 4.5 2.0 1.0 CB A:LEU75 4.5 2.8 1.0 N A:GLY80 4.6 14.7 1.0 CB A:ASN77 4.6 14.4 1.0 CB A:ALA74 4.6 7.2 1.0 N A:THR79 4.7 15.8 1.0 O A:ALA74 4.7 7.2 1.0 O A:GLY80 4.7 10.2 1.0 CA A:ASN77 4.7 25.6 1.0 CA A:ASP41 4.7 2.0 1.0 CA A:ASP76 4.8 10.0 1.0 C A:ASN77 4.8 25.6 1.0 O A:ASP41 4.8 9.9 1.0 CG2 A:THR79 4.9 20.9 1.0 CA A:THR79 4.9 15.8 1.0 O A:ASN77 4.9 14.4 1.0 C A:ASP76 5.0 10.0 1.0 CB A:GLN2 5.0 5.6 1.0

V.S.Stoll, B.T.Eger, R.C.Hynes, V.Martichonok, J.B.Jones, E.F.Pai. Differences in Binding Modes of Enantiomers of 1-Acetamido Boronic Acid Based Protease Inhibitors: Crystal Structures of Gamma-Chymotrypsin and Subtilisin Carlsberg Complexes. Biochemistry V. 37 451 1998.
ISSN: ISSN 0006-2960
PubMed: 9425066
DOI: 10.1021/BI971166O