Calcium in PDB 1fj3: Thermolysin (50% Acetone Soaked)

All present enzymatic activity of Thermolysin (50% Acetone Soaked):
3.4.24.27;

The structure of Thermolysin (50% Acetone Soaked), PDB code: 1fj3 was solved by A.C.English, C.R.Groom, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.010, 94.010, 131.030, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 20.5

The structure of Thermolysin (50% Acetone Soaked) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (50% Acetone Soaked) (pdb code 1fj3). 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 (50% Acetone Soaked), PDB code: 1fj3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (50% Acetone Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (50% Acetone Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.2 occ:1.00 O A:GLU187 2.6 20.6 1.0 OD2 A:ASP138 2.6 23.3 1.0 OE1 A:GLU190 2.6 19.4 1.0 OE2 A:GLU190 2.6 18.3 1.0 OD1 A:ASP185 2.7 20.8 1.0 OE1 A:GLU177 2.7 23.7 1.0 O A:HOH520 2.7 21.6 1.0 OE2 A:GLU177 2.9 20.1 1.0 CD A:GLU190 3.1 29.8 1.0 CD A:GLU177 3.2 24.1 1.0 CG A:ASP138 3.5 26.2 1.0 C A:GLU187 3.6 22.8 1.0 CG A:ASP185 3.6 34.0 1.0 CA A:CA502 3.8 27.6 1.0 OD2 A:ASP185 3.8 21.1 1.0 CB A:ASP138 4.0 19.9 1.0 N A:GLU187 4.2 24.8 1.0 O A:ASP185 4.3 23.9 1.0 CA A:ILE188 4.3 18.6 1.0 OD1 A:ASP138 4.4 23.0 1.0 CA A:GLU187 4.4 24.9 1.0 N A:ILE188 4.4 18.1 1.0 N A:GLY189 4.5 22.0 1.0 CG A:GLU190 4.5 21.7 1.0 CG A:GLU177 4.6 18.8 1.0 CB A:GLU187 4.6 26.5 1.0 C A:ASP185 4.7 25.1 1.0 O A:HOH535 4.7 27.6 1.0 N A:ASP185 4.8 21.5 1.0 C A:ILE188 4.8 22.7 1.0 CB A:ASP185 4.9 22.7 1.0 N A:GLU190 4.9 19.8 1.0 O A:HOH536 5.0 31.6 1.0 CB A:GLU177 5.0 21.3 1.0

Calcium binding site 2 out of 4 in the Thermolysin (50% Acetone Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (50% Acetone Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:27.6 occ:1.00 O A:HOH536 2.4 31.6 1.0 OD2 A:ASP185 2.5 21.1 1.0 OE2 A:GLU177 2.5 20.1 1.0 OE2 A:GLU190 2.5 18.3 1.0 O A:HOH519 2.6 28.7 1.0 O A:ASN183 2.6 28.3 1.0 CD A:GLU177 3.4 24.1 1.0 CG A:ASP185 3.4 34.0 1.0 CD A:GLU190 3.5 29.8 1.0 OD1 A:ASP185 3.7 20.8 1.0 C A:ASN183 3.8 31.5 1.0 CA A:CA501 3.8 24.2 1.0 OE1 A:GLU177 3.8 23.7 1.0 O A:LYS182 3.9 31.8 1.0 CG A:GLU190 4.0 21.7 1.0 N A:ASP185 4.2 21.5 1.0 C A:PRO184 4.2 28.2 1.0 CA A:PRO184 4.2 28.6 1.0 OD2 A:ASP191 4.3 26.0 1.0 OD1 A:ASP191 4.3 26.0 1.0 OE1 A:GLU190 4.3 19.4 1.0 CG A:GLU177 4.4 18.8 1.0 CB A:ASN183 4.4 40.5 1.0 N A:PRO184 4.4 31.2 1.0 CB A:ASP185 4.5 22.7 1.0 CG A:ASP191 4.7 26.9 1.0 CA A:ASN183 4.7 30.5 1.0 CA A:ASP185 4.9 22.7 1.0 O A:PRO184 4.9 25.7 1.0 C A:LYS182 5.0 34.4 1.0

Calcium binding site 3 out of 4 in the Thermolysin (50% Acetone Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (50% Acetone Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:25.0 occ:1.00 O A:GLN61 2.5 21.1 1.0 OD1 A:ASP59 2.5 21.2 1.0 O A:HOH533 2.6 22.4 1.0 OD1 A:ASP57 2.6 21.8 1.0 O A:HOH522 2.6 29.4 1.0 O A:HOH553 2.7 32.5 1.0 OD2 A:ASP57 2.7 22.0 1.0 CG A:ASP57 3.1 26.6 1.0 CG A:ASP59 3.6 32.1 1.0 C A:GLN61 3.7 26.4 1.0 OD2 A:ASP59 3.8 27.2 1.0 N A:GLN61 3.9 22.8 1.0 O A:HOH558 4.1 38.6 1.0 CA A:GLN61 4.2 23.9 1.0 N A:ASP59 4.3 23.6 1.0 CB A:GLN61 4.3 27.3 1.0 CB A:ASP57 4.6 20.8 1.0 N A:ASN60 4.6 22.2 1.0 N A:PHE62 4.6 20.4 1.0 O A:HOH550 4.7 29.0 1.0 O A:HOH605 4.7 51.7 1.0 OD2 A:ASP67 4.7 21.1 1.0 CA A:PHE62 4.7 20.9 1.0 O A:HOH515 4.7 22.1 1.0 N A:ALA58 4.7 20.2 1.0 CB A:ASP59 4.8 22.5 1.0 CA A:ASP59 4.8 22.6 1.0 C A:ASP59 4.8 23.7 1.0

Calcium binding site 4 out of 4 in the Thermolysin (50% Acetone Soaked)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (50% Acetone Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:28.6 occ:1.00 OD1 A:ASP200 2.6 26.2 1.0 O A:HOH571 2.6 30.1 1.0 O A:TYR193 2.7 22.2 1.0 O A:THR194 2.7 28.9 1.0 O A:ILE197 2.7 35.7 1.0 O A:HOH544 2.7 43.1 1.0 OG1 A:THR194 2.9 32.7 1.0 C A:THR194 3.4 29.2 1.0 CG A:ASP200 3.6 24.8 1.0 C A:TYR193 3.6 26.5 1.0 CB A:THR194 3.7 30.7 1.0 OD2 A:ASP200 3.8 28.6 1.0 CA A:THR194 3.8 26.4 1.0 C A:ILE197 3.9 42.9 1.0 N A:THR194 4.0 23.5 1.0 N A:ILE197 4.3 43.3 1.0 CB A:ILE197 4.3 42.8 1.0 CA A:ILE197 4.4 42.8 1.0 N A:PRO195 4.4 30.6 1.0 O A:ASP200 4.5 26.8 1.0 N A:ASP200 4.6 30.2 1.0 CA A:TYR193 4.7 22.4 1.0 O A:GLU190 4.7 23.2 1.0 CD2 A:TYR193 4.7 29.7 1.0 CB A:TYR193 4.7 23.3 1.0 N A:SER198 4.8 41.1 1.0 CA A:SER198 4.8 41.8 1.0 CB A:ASP200 4.9 27.2 1.0 C A:ASP200 4.9 25.1 1.0 CA A:PRO195 4.9 33.5 1.0 CG2 A:THR194 5.0 26.2 1.0 C A:SER198 5.0 40.4 1.0 CG2 A:ILE197 5.0 38.1 1.0

A.C.English, C.R.Groom, R.E.Hubbard. Experimental and Computational Mapping of the Binding Surface of A Crystalline Protein. Protein Eng. V. 14 47 2001.
ISSN: ISSN 0269-2139
PubMed: 11287678
DOI: 10.1093/PROTEIN/14.1.47