Sodium in PDB 1av7: Subtilisin Carlsberg L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex

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

The structure of Subtilisin Carlsberg L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 1av7 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)	10.00 / 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 (%)	14.8 / 27.3

The binding sites of Sodium atom in the Subtilisin Carlsberg L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex (pdb code 1av7). 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 L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex, PDB code: 1av7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Subtilisin Carlsberg L-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 L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:30.2 occ:1.00 O A:VAL174 2.4 5.0 1.0 O A:TYR171 2.8 12.2 1.0 O A:ALA169 2.8 5.0 1.0 C A:VAL174 3.6 5.0 1.0 O A:GLU195 3.8 13.0 1.0 N A:ALA176 3.8 5.0 1.0 C A:TYR171 3.9 9.7 1.0 O A:LYS170 3.9 7.5 1.0 C A:ALA169 4.1 5.0 1.0 CB A:ALA176 4.1 7.8 1.0 CB A:GLU195 4.2 20.4 1.0 OE1 A:GLU197 4.2 10.7 1.0 C A:LYS170 4.2 8.3 1.0 NH2 A:ARG247 4.3 11.8 1.0 CA A:ASP172 4.3 17.3 1.0 CA A:ILE175 4.4 5.0 1.0 C A:ILE175 4.4 5.0 1.0 N A:ILE175 4.4 5.0 1.0 CA A:ALA176 4.6 5.0 1.0 N A:ASP172 4.6 15.4 1.0 CA A:VAL174 4.7 5.0 1.0 N A:TYR171 4.7 9.0 1.0 C A:GLU195 4.7 7.7 1.0 N A:VAL174 4.7 5.0 1.0 CA A:LYS170 4.8 8.2 1.0 N A:LYS170 4.9 5.2 1.0 CA A:TYR171 4.9 11.8 1.0 C A:ASP172 5.0 15.8 1.0 CA A:GLU195 5.0 13.2 1.0 CB A:VAL174 5.0 5.0 1.0

Sodium binding site 2 out of 2 in the Subtilisin Carlsberg L-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 L-Naphthyl-1-Acetamido Boronic Acid Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:13.8 occ:1.00 O A:LEU75 2.2 5.5 1.0 NE2 A:GLN2 2.2 7.0 1.0 O A:VAL81 2.3 5.0 1.0 OD1 A:ASN77 2.4 5.0 1.0 OD1 A:ASP41 2.4 8.1 1.0 O A:THR79 2.5 8.1 1.0 OD2 A:ASP41 2.5 9.6 1.0 CG A:ASP41 2.8 7.2 1.0 CG A:ASN77 3.3 5.0 1.0 CD A:GLN2 3.4 6.9 1.0 C A:LEU75 3.5 5.0 1.0 C A:VAL81 3.6 5.0 1.0 C A:THR79 3.6 5.9 1.0 N A:ASN77 3.8 5.0 1.0 CG A:GLN2 3.9 5.0 1.0 ND2 A:ASN77 3.9 5.0 1.0 N A:VAL81 3.9 5.0 1.0 C A:GLY80 4.2 5.3 1.0 CB A:ASP41 4.3 5.0 1.0 N A:THR79 4.3 8.2 1.0 CA A:LEU75 4.3 5.0 1.0 N A:GLY80 4.4 9.5 1.0 N A:ASP76 4.4 5.0 1.0 CA A:GLY80 4.4 5.3 1.0 CA A:VAL81 4.4 5.0 1.0 CA A:ASN77 4.4 5.0 1.0 CG2 A:THR79 4.5 17.5 1.0 CB A:ASN77 4.5 5.0 1.0 OE1 A:GLN2 4.5 9.4 1.0 CA A:ASP76 4.5 5.0 1.0 N A:LEU82 4.5 5.0 1.0 N A:LEU75 4.5 5.0 1.0 C A:ASP76 4.5 5.0 1.0 CA A:THR79 4.6 5.2 1.0 C A:ASN77 4.6 5.0 1.0 CB A:LEU75 4.6 5.0 1.0 CA A:LEU82 4.6 5.0 1.0 C A:ALA74 4.7 5.0 1.0 CB A:GLN2 4.7 5.4 1.0 O A:ASN77 4.7 5.0 1.0 O A:ALA74 4.8 5.0 1.0 O A:GLY80 4.9 9.0 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