Calcium in PDB 7akn: Thermolysin From Bacillus Thermoproteolyticus

All present enzymatic activity of Thermolysin From Bacillus Thermoproteolyticus:
3.4.24.27;

The structure of Thermolysin From Bacillus Thermoproteolyticus, PDB code: 7akn was solved by A.S.Boikova, K.B.Ilina, M.A.Marchenkova, Y.V.Pisarevsky, V.I.Timofeev, M.V.Kovalchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 2.46
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.408, 92.408, 129.330, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 22.3

The structure of Thermolysin From Bacillus Thermoproteolyticus also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin From Bacillus Thermoproteolyticus (pdb code 7akn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin From Bacillus Thermoproteolyticus, PDB code: 7akn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:40.9 occ:1.00 O A:GLU187 2.3 39.9 1.0 OE1 A:GLU177 2.4 53.3 1.0 OD1 A:ASP185 2.4 49.6 1.0 OE1 A:GLU190 2.5 42.2 1.0 OE2 A:GLU190 2.5 39.6 1.0 O A:HOH511 2.5 37.5 1.0 OD2 A:ASP138 2.6 41.9 1.0 OE2 A:GLU177 2.7 48.6 1.0 CD A:GLU190 2.8 46.1 1.0 CD A:GLU177 2.9 47.2 1.0 C A:GLU187 3.5 44.2 1.0 CG A:ASP138 3.5 45.4 1.0 CG A:ASP185 3.5 51.8 1.0 OD2 A:ASP185 4.0 57.9 1.0 CB A:ASP138 4.0 40.3 1.0 O A:ASP185 4.1 47.2 1.0 O A:HOH543 4.2 32.5 1.0 CG A:GLU190 4.3 45.7 1.0 N A:GLU187 4.3 36.0 1.0 N A:ILE188 4.3 43.4 1.0 CG A:GLU177 4.3 42.5 1.0 N A:GLY189 4.4 42.6 1.0 CA A:GLU187 4.4 44.2 1.0 CA A:ILE188 4.4 46.9 1.0 OD1 A:ASP138 4.4 48.0 1.0 C A:ASP185 4.5 44.3 1.0 CA A:CA402 4.6 96.9 1.0 N A:ASP185 4.7 45.0 1.0 CB A:GLU187 4.8 48.5 1.0 CB A:ASP185 4.8 45.6 1.0 C A:ILE188 4.8 43.7 1.0 CA A:ASP185 4.9 43.1 1.0 CB A:GLU177 4.9 39.1 1.0 N A:GLU190 4.9 42.5 1.0

Calcium binding site 2 out of 4 in the Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:96.9 occ:1.00 O A:ASN183 2.6 52.5 1.0 OE2 A:GLU190 3.0 39.6 1.0 OE2 A:GLU177 3.5 48.6 1.0 C A:ASN183 3.6 55.4 1.0 OD2 A:ASP185 3.6 57.9 1.0 OD1 A:ASP191 3.6 56.0 1.0 CD A:GLU190 3.7 46.1 1.0 O A:HOH540 3.8 48.0 1.0 CG A:GLU190 3.8 45.7 1.0 CD A:GLU177 3.9 47.2 1.0 OD2 A:ASP191 3.9 54.0 1.0 CG A:ASP191 4.1 54.3 1.0 CG A:ASP185 4.1 51.8 1.0 OE1 A:GLU177 4.3 53.3 1.0 CA A:PRO184 4.4 48.3 1.0 N A:PRO184 4.4 46.8 1.0 CA A:ASN183 4.4 61.8 1.0 OD1 A:ASP185 4.4 49.6 1.0 CB A:ASN183 4.4 62.9 1.0 CA A:CA401 4.6 40.9 1.0 C A:PRO184 4.6 46.4 1.0 N A:ASP185 4.7 45.0 1.0 N A:ASN183 4.7 64.3 1.0 CG A:GLU177 4.8 42.5 1.0 OE1 A:GLU190 4.8 42.2 1.0 CB A:ASP185 5.0 45.6 1.0

Calcium binding site 3 out of 4 in the Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:51.2 occ:1.00 OD2 A:ASP57 2.3 46.3 1.0 O A:GLN61 2.4 40.3 1.0 O A:HOH513 2.4 46.7 1.0 O A:HOH596 2.5 32.6 1.0 OD1 A:ASP57 2.6 49.8 1.0 O A:HOH505 2.6 38.8 1.0 OD1 A:ASP59 2.7 57.4 1.0 CG A:ASP57 2.8 42.9 1.0 CG A:ASP59 3.3 54.3 1.0 OD2 A:ASP59 3.4 57.4 1.0 C A:GLN61 3.6 39.5 1.0 O A:HOH573 3.9 37.7 1.0 N A:GLN61 4.2 40.0 1.0 CB A:ASP57 4.3 42.7 1.0 CA A:GLN61 4.3 40.9 1.0 O A:HOH506 4.5 39.5 1.0 N A:ASP59 4.5 43.0 1.0 CB A:GLN61 4.6 42.9 1.0 CB A:ASP59 4.6 46.7 1.0 N A:PHE62 4.6 33.0 1.0 OD2 A:ASP67 4.6 36.9 1.0 N A:ALA58 4.7 41.5 1.0 N A:ASN60 4.9 38.8 1.0 CA A:ASP57 4.9 41.5 1.0 CA A:PHE62 5.0 35.5 1.0 CA A:ASP59 5.0 45.1 1.0

Calcium binding site 4 out of 4 in the Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:50.2 occ:1.00 O A:THR194 2.2 54.2 1.0 O A:ILE197 2.3 54.9 1.0 O A:HOH545 2.3 46.1 1.0 OG1 A:THR194 2.4 49.8 1.0 OD1 A:ASP200 2.5 47.7 1.0 O A:TYR193 2.5 45.8 1.0 O A:HOH509 2.5 52.1 1.0 C A:THR194 3.2 57.0 1.0 C A:TYR193 3.4 43.8 1.0 CB A:THR194 3.5 55.0 1.0 C A:ILE197 3.5 56.6 1.0 CG A:ASP200 3.5 51.8 1.0 CA A:THR194 3.6 52.8 1.0 N A:THR194 3.9 47.7 1.0 OD2 A:ASP200 3.9 64.7 1.0 CA A:ILE197 4.2 65.1 1.0 N A:PRO195 4.3 54.0 1.0 N A:ILE197 4.3 68.4 1.0 O A:ASP200 4.3 45.9 1.0 CB A:ILE197 4.4 65.4 1.0 O A:GLU190 4.4 47.2 1.0 N A:SER198 4.4 55.8 1.0 CA A:SER198 4.6 57.6 1.0 CA A:TYR193 4.6 45.7 1.0 CA A:PRO195 4.6 57.6 1.0 CG2 A:THR194 4.7 55.5 1.0 N A:ASP200 4.8 50.3 1.0 CB A:TYR193 4.8 45.7 1.0 CB A:ASP200 4.8 46.2 1.0 C A:ASP200 4.9 46.0 1.0 C A:SER198 4.9 55.9 1.0 CD2 A:TYR193 4.9 53.8 1.0 C A:PRO195 4.9 58.6 1.0 CG2 A:ILE197 5.0 61.9 1.0

A.S.Boikova, K.B.Ilina, M.A.Marchenkova, Y.V.Pisarevsky, V.I.Timofeev, M.V.Kovalchuk. Thermolysin From Bacillus Thermoproteolyticus To Be Published.