Sodium in PDB 1dbi: Crystal Structure of A Thermostable Serine Protease

The structure of Crystal Structure of A Thermostable Serine Protease, PDB code: 1dbi was solved by C.A.Smith, H.S.Toogood, H.M.Baker, R.M.Daniel, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.050, 51.680, 52.780, 90.00, 96.10, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of A Thermostable Serine Protease also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of A Thermostable Serine Protease (pdb code 1dbi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Thermostable Serine Protease, PDB code: 1dbi:

Sodium binding site 1 out of 1 in the Crystal Structure of A Thermostable Serine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Thermostable Serine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:9.9 occ:1.00 O A:HOH303 2.2 38.4 1.0 O A:HOH301 2.5 21.3 1.0 O A:VAL179 2.6 11.7 1.0 O A:HOH302 2.7 25.0 1.0 OD2 A:ASP202 2.9 18.3 1.0 O A:TYR176 3.0 11.6 1.0 OD1 A:ASP202 3.6 18.9 1.0 CG A:ASP202 3.6 17.3 1.0 O A:HOH569 3.7 13.4 1.0 C A:VAL179 3.8 12.8 1.0 O A:GLU177 3.8 13.6 1.0 C A:TYR176 4.1 6.9 1.0 C A:GLU177 4.2 16.1 1.0 N A:VAL179 4.3 9.2 1.0 CA A:GLU177 4.4 7.8 1.0 CA A:ILE180 4.6 8.3 1.0 N A:ILE180 4.6 8.7 1.0 N A:ALA181 4.7 8.2 1.0 CA A:VAL179 4.7 6.9 1.0 O A:HOH496 4.7 19.0 1.0 N A:GLU177 4.8 7.2 1.0 O A:TRP200 4.8 18.3 1.0 N A:ASN178 4.9 9.6 1.0

C.A.Smith, H.S.Toogood, H.M.Baker, R.M.Daniel, E.N.Baker. Calcium-Mediated Thermostability in the Subtilisin Superfamily: the Crystal Structure of Bacillus Ak.1 Protease at 1.8 A Resolution. J.Mol.Biol. V. 294 1027 1999.
ISSN: ISSN 0022-2836
PubMed: 10588904
DOI: 10.1006/JMBI.1999.3291