Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Thermostable Serine Protease (pdb code 1dbi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Thermostable Serine Protease, PDB code: 1dbi:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Thermostable Serine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Thermostable Serine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:9.5 occ:1.00 O A:THR88 2.1 12.8 1.0 O A:GLU83 2.1 12.6 1.0 OD2 A:ASP5 2.3 15.2 1.0 OD1 A:ASN86 2.3 10.2 1.0 OD1 A:ASP48 2.4 9.9 1.0 OD2 A:ASP48 2.5 9.9 1.0 O A:ILE90 2.5 13.3 1.0 CG A:ASP48 2.8 11.6 1.0 C A:GLU83 3.3 9.3 1.0 C A:THR88 3.3 11.0 1.0 CG A:ASN86 3.3 14.9 1.0 CG A:ASP5 3.4 14.6 1.0 C A:ILE90 3.6 17.0 1.0 N A:ILE90 3.7 11.1 1.0 ND2 A:ASN86 3.8 15.4 1.0 CB A:ASP5 4.0 12.0 1.0 N A:THR84 4.2 8.5 1.0 N A:GLY89 4.2 12.8 1.0 CA A:THR88 4.2 10.8 1.0 CA A:THR84 4.2 8.5 1.0 C A:GLY89 4.3 16.9 1.0 CA A:ILE90 4.3 10.5 1.0 CB A:ASP48 4.3 12.7 1.0 CB A:THR88 4.3 11.2 1.0 OD1 A:ASP5 4.3 18.8 1.0 CA A:GLU83 4.3 14.2 1.0 CA A:GLY89 4.4 14.1 1.0 N A:THR88 4.4 9.5 1.0 CB A:GLU83 4.5 15.8 1.0 N A:GLU83 4.5 12.8 1.0 N A:ALA91 4.6 10.7 1.0 CB A:ASN86 4.7 16.7 1.0 N A:ASN86 4.7 14.1 1.0 CG2 A:THR88 4.8 12.9 1.0 C A:THR84 4.9 10.0 1.0 N A:ASN85 4.9 9.5 1.0 CA A:ASP5 4.9 12.9 1.0 CB A:ALA82 4.9 10.4 1.0 CA A:ALA91 4.9 8.9 1.0 CA A:ASP48 5.0 14.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Thermostable Serine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Thermostable Serine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:13.6 occ:1.00 OD2 A:ASP58 2.2 14.0 1.0 O A:HOH304 2.3 14.1 1.0 O A:ASP65 2.3 12.0 1.0 OD1 A:ASP63 2.4 19.9 1.0 O A:HOH306 2.4 14.6 1.0 O A:HOH305 2.4 20.6 1.0 OD2 A:ASP63 2.8 23.9 1.0 CG A:ASP63 2.9 22.5 1.0 CG A:ASP58 3.3 12.1 1.0 C A:ASP65 3.5 17.1 1.0 CB A:ASP58 3.8 13.8 1.0 CB A:ASP65 4.0 11.4 1.0 CA A:ASP65 4.3 7.0 1.0 OD2 A:ASP65 4.3 14.8 1.0 OD1 A:ASP58 4.3 11.4 1.0 NH1 A:ARG103 4.3 20.6 1.0 CB A:ASP61 4.4 16.0 1.0 CG A:ASP65 4.4 14.7 1.0 CB A:ASP63 4.5 15.9 1.0 OD1 A:ASP61 4.5 19.9 1.0 N A:PRO66 4.5 19.5 1.0 N A:ASP65 4.5 7.3 1.0 CA A:PRO66 4.7 15.8 1.0 N A:MET67 4.8 6.5 1.0 CD A:ARG103 4.8 11.6 1.0 CG A:ASP61 4.9 23.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Thermostable Serine Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Thermostable Serine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:15.9 occ:1.00 O A:PRO47 2.2 16.2 1.0 OD1 A:ASP50 2.2 14.5 1.0 O A:HOH309 2.3 19.7 1.0 O A:HOH308 2.3 30.0 1.0 O A:HOH307 2.4 17.1 1.0 OE1 A:GLU83 2.4 19.4 1.0 OE2 A:GLU83 2.6 9.6 1.0 CD A:GLU83 2.8 32.3 1.0 C A:PRO47 3.3 18.3 1.0 CG A:ASP50 3.4 20.9 1.0 OD2 A:ASP50 3.9 16.4 1.0 CA A:PRO47 3.9 11.7 1.0 O A:HOH595 4.2 44.1 1.0 N A:GLY51 4.2 13.6 1.0 N A:ASP48 4.3 15.0 1.0 CG A:GLU83 4.3 23.6 1.0 N A:ASP50 4.4 8.4 1.0 CA A:ASP48 4.6 14.0 1.0 CB A:ASP50 4.6 11.5 1.0 ND2 A:ASN86 4.6 15.4 1.0 O A:HOH533 4.7 21.2 1.0 CA A:ASP50 4.7 9.9 1.0 N A:LEU49 4.8 11.3 1.0 O A:HIS46 4.8 12.7 1.0 C A:ASP50 4.8 18.3 1.0 CB A:PRO47 4.8 13.1 1.0 C A:ASP48 4.9 15.7 1.0 CA A:GLY51 4.9 10.6 1.0 CB A:GLU83 5.0 15.8 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