Calcium in PDB 1bqb: Aureolysin, Staphylococcus Aureus Metalloproteinase

All present enzymatic activity of Aureolysin, Staphylococcus Aureus Metalloproteinase:
3.4.24.27;

The structure of Aureolysin, Staphylococcus Aureus Metalloproteinase, PDB code: 1bqb was solved by F.J.Medrano, A.Banbula, J.Potempa, J.Travis, W.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.700, 79.500, 100.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.9

The structure of Aureolysin, Staphylococcus Aureus Metalloproteinase also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Aureolysin, Staphylococcus Aureus Metalloproteinase (pdb code 1bqb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Aureolysin, Staphylococcus Aureus Metalloproteinase, PDB code: 1bqb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Aureolysin, Staphylococcus Aureus Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Aureolysin, Staphylococcus Aureus Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca351 b:13.2 occ:1.00 O A:LEU184 2.2 14.5 1.0 OD2 A:ASP179 2.3 10.8 1.0 OD2 A:ASP140 2.3 10.9 1.0 O A:HOH448 2.4 10.2 1.0 OD1 A:ASP182 2.4 11.6 1.0 OE2 A:GLU187 2.6 12.6 1.0 OE1 A:GLU187 2.6 11.1 1.0 CD A:GLU187 3.0 11.6 1.0 C A:LEU184 3.3 13.9 1.0 CG A:ASP182 3.4 11.7 1.0 CG A:ASP140 3.4 10.5 1.0 CG A:ASP179 3.5 10.6 1.0 OD2 A:ASP182 3.6 11.3 1.0 CA A:CA352 3.8 12.9 1.0 CB A:ASP140 3.9 10.7 1.0 N A:MET185 4.2 14.0 1.0 N A:LEU184 4.2 14.8 1.0 CA A:LEU184 4.2 14.3 1.0 CA A:MET185 4.3 14.8 1.0 CB A:ASP179 4.3 11.3 1.0 OD1 A:ASP140 4.3 11.8 1.0 OD1 A:ASP179 4.4 11.9 1.0 O A:ASP182 4.4 14.2 1.0 O A:HOH440 4.4 11.7 1.0 O A:ASP179 4.5 14.3 1.0 CG A:GLU187 4.5 10.7 1.0 CB A:LEU184 4.5 14.3 1.0 N A:GLY186 4.5 14.1 1.0 O A:HOH516 4.6 42.7 1.0 CB A:ASP182 4.7 12.1 1.0 C A:MET185 4.8 14.1 1.0 C A:ASP182 4.8 13.9 1.0 O A:HOH406 4.9 12.2 1.0

Calcium binding site 2 out of 3 in the Aureolysin, Staphylococcus Aureus Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Aureolysin, Staphylococcus Aureus Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca352 b:12.9 occ:1.00 OE2 A:GLU181 2.2 19.1 1.0 O A:HOH405 2.2 13.7 1.0 O A:HOH406 2.3 12.2 1.0 OD2 A:ASP182 2.4 11.3 1.0 OE2 A:GLU187 2.4 12.6 1.0 OD2 A:ASP179 2.6 10.8 1.0 OD1 A:ASP179 2.7 11.9 1.0 CG A:ASP179 3.0 10.6 1.0 CD A:GLU181 3.2 19.2 1.0 CG A:ASP182 3.5 11.7 1.0 CG A:GLU181 3.5 18.0 1.0 CD A:GLU187 3.6 11.6 1.0 CA A:CA351 3.8 13.2 1.0 OD1 A:ASP182 3.9 11.6 1.0 O A:HOH511 4.1 36.2 1.0 CG A:GLU187 4.3 10.7 1.0 OE1 A:GLU181 4.3 20.7 1.0 OD1 A:ASP188 4.4 15.2 1.0 O A:HOH447 4.4 28.0 1.0 OD2 A:ASP188 4.5 15.9 1.0 OE1 A:GLU187 4.5 11.1 1.0 CB A:ASP179 4.5 11.3 1.0 O A:HOH440 4.6 11.7 1.0 OD1 A:ASN139 4.7 12.5 1.0 CB A:ASP182 4.8 12.1 1.0 CG A:ASP188 4.8 15.3 1.0 CB A:GLU181 5.0 16.7 1.0

Calcium binding site 3 out of 3 in the Aureolysin, Staphylococcus Aureus Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Aureolysin, Staphylococcus Aureus Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca353 b:15.7 occ:1.00 O A:HOH421 2.1 22.5 1.0 O A:HOH420 2.3 13.8 1.0 O A:LYS194 2.3 18.7 1.0 O A:TYR190 2.3 12.0 1.0 OD1 A:ASP197 2.4 17.5 1.0 OG1 A:THR191 2.5 15.3 1.0 O A:THR191 2.5 15.0 1.0 C A:THR191 3.3 14.8 1.0 C A:TYR190 3.4 12.6 1.0 C A:LYS194 3.5 18.8 1.0 CG A:ASP197 3.5 17.7 1.0 CB A:THR191 3.6 14.6 1.0 CA A:THR191 3.7 14.6 1.0 OD2 A:ASP197 3.9 18.6 1.0 N A:THR191 3.9 13.4 1.0 CA A:LYS194 4.2 18.2 1.0 CB A:LYS194 4.2 17.3 1.0 N A:LYS194 4.3 18.2 1.0 N A:PRO192 4.3 15.7 1.0 O A:GLU187 4.4 15.0 1.0 O A:ASP197 4.5 16.9 1.0 N A:GLU195 4.5 19.7 1.0 CA A:TYR190 4.6 13.0 1.0 N A:ASP197 4.7 18.2 1.0 CA A:GLU195 4.7 21.0 1.0 CD2 A:TYR190 4.7 17.4 1.0 CA A:PRO192 4.8 16.9 1.0 CG A:LYS194 4.8 17.3 1.0 CB A:TYR190 4.8 14.0 1.0 CB A:ASP197 4.8 16.6 1.0 CG2 A:THR191 4.8 15.0 1.0 C A:ASP197 4.9 16.8 1.0 C A:GLU195 5.0 21.5 1.0

A.Banbula, J.Potempa, J.Travis, C.Fernandez-Catalan, K.Mann, R.Huber, W.Bode, F.Medrano. Amino-Acid Sequence and Three-Dimensional Structure of the Staphylococcus Aureus Metalloproteinase at 1.72 A Resolution. Structure V. 6 1185 1998.
ISSN: ISSN 0969-2126
PubMed: 9753696
DOI: 10.1016/S0969-2126(98)00118-X