Calcium in PDB 1fjw: Thermolysin (50 Mm Phenol Soaked)

All present enzymatic activity of Thermolysin (50 Mm Phenol Soaked):
3.4.24.27;

The structure of Thermolysin (50 Mm Phenol Soaked), PDB code: 1fjw 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)	15.00 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.960, 93.960, 130.915, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 19.4

The structure of Thermolysin (50 Mm Phenol Soaked) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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

Calcium binding site 1 out of 4 in the Thermolysin (50 Mm Phenol 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 Mm Phenol Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.8 occ:1.00 O A:GLU187 2.5 21.1 1.0 OD2 A:ASP138 2.6 24.6 1.0 O A:HOH522 2.6 22.1 1.0 OE1 A:GLU190 2.6 20.0 1.0 OE2 A:GLU190 2.6 19.3 1.0 OE1 A:GLU177 2.6 21.9 1.0 OD1 A:ASP185 2.6 21.7 1.0 OE2 A:GLU177 2.8 21.9 1.0 CD A:GLU190 3.1 25.9 1.0 CD A:GLU177 3.1 24.5 1.0 CG A:ASP138 3.5 24.9 1.0 C A:GLU187 3.6 22.9 1.0 CG A:ASP185 3.6 30.2 1.0 CA A:CA503 3.9 27.9 1.0 OD2 A:ASP185 3.9 23.7 1.0 CB A:ASP138 4.0 19.0 1.0 O A:ASP185 4.2 24.4 1.0 N A:GLU187 4.3 25.0 1.0 CA A:ILE188 4.3 20.4 1.0 OD1 A:ASP138 4.3 22.9 1.0 O A:HOH643 4.3 41.1 1.0 N A:ILE188 4.4 19.4 1.0 CA A:GLU187 4.4 25.1 1.0 O A:HOH537 4.5 28.2 1.0 N A:GLY189 4.5 22.6 1.0 CG A:GLU177 4.5 19.2 1.0 CG A:GLU190 4.6 23.3 1.0 C A:ASP185 4.7 25.3 1.0 CB A:GLU187 4.7 25.8 1.0 N A:ASP185 4.7 24.2 1.0 C A:ILE188 4.8 21.2 1.0 CB A:ASP185 4.9 23.3 1.0 N A:GLU190 4.9 21.4 1.0 CB A:GLU177 5.0 21.6 1.0 O A:HOH538 5.0 52.4 1.0

Calcium binding site 2 out of 4 in the Thermolysin (50 Mm Phenol 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 Mm Phenol Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:27.9 occ:1.00 O A:HOH538 2.5 52.4 1.0 O A:HOH521 2.5 35.8 1.0 OD2 A:ASP185 2.6 23.7 1.0 OE2 A:GLU190 2.6 19.3 1.0 O A:ASN183 2.6 29.2 1.0 OE2 A:GLU177 2.6 21.9 1.0 CG A:ASP185 3.3 30.2 1.0 CD A:GLU177 3.4 24.5 1.0 CD A:GLU190 3.5 25.9 1.0 OD1 A:ASP185 3.7 21.7 1.0 C A:ASN183 3.8 33.4 1.0 O A:LYS182 3.9 33.0 1.0 CA A:CA502 3.9 22.8 1.0 OE1 A:GLU177 3.9 21.9 1.0 CG A:GLU190 4.1 23.3 1.0 N A:ASP185 4.1 24.2 1.0 C A:PRO184 4.2 30.0 1.0 CA A:PRO184 4.2 29.9 1.0 OD2 A:ASP191 4.2 24.6 1.0 CB A:ASN183 4.3 37.5 1.0 OD1 A:ASP191 4.3 25.8 1.0 CG A:GLU177 4.3 19.2 1.0 OE1 A:GLU190 4.4 20.0 1.0 N A:PRO184 4.4 32.4 1.0 CB A:ASP185 4.5 23.3 1.0 O A:HOH643 4.6 41.1 1.0 CG A:ASP191 4.6 30.9 1.0 CA A:ASN183 4.7 30.5 1.0 O A:PRO184 4.9 28.0 1.0 C A:LYS182 4.9 35.1 1.0 CA A:ASP185 4.9 23.4 1.0 O A:HOH612 5.0 47.1 1.0

Calcium binding site 3 out of 4 in the Thermolysin (50 Mm Phenol 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 Mm Phenol Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:24.4 occ:1.00 O A:HOH535 2.5 23.0 1.0 O A:GLN61 2.5 22.2 1.0 O A:HOH524 2.5 29.4 1.0 OD1 A:ASP59 2.5 22.0 1.0 OD1 A:ASP57 2.6 21.6 1.0 O A:HOH555 2.6 33.4 1.0 OD2 A:ASP57 2.7 23.9 1.0 CG A:ASP57 3.1 25.3 1.0 CG A:ASP59 3.6 32.3 1.0 C A:GLN61 3.7 24.5 1.0 OD2 A:ASP59 3.8 27.4 1.0 N A:GLN61 3.9 23.7 1.0 O A:HOH560 4.1 38.3 1.0 CA A:GLN61 4.2 24.1 1.0 N A:ASP59 4.3 25.2 1.0 CB A:GLN61 4.3 27.6 1.0 CB A:ASP57 4.6 21.2 1.0 O A:HOH608 4.6 65.4 1.0 N A:PHE62 4.6 22.0 1.0 N A:ASN60 4.6 22.1 1.0 O A:HOH552 4.6 28.0 1.0 OD2 A:ASP67 4.7 23.0 1.0 CA A:PHE62 4.7 21.5 1.0 O A:HOH517 4.7 21.4 1.0 CB A:ASP59 4.7 22.5 1.0 N A:ALA58 4.8 20.3 1.0 C A:ASP59 4.8 25.5 1.0 CA A:ASP59 4.8 23.9 1.0

Calcium binding site 4 out of 4 in the Thermolysin (50 Mm Phenol 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 Mm Phenol Soaked) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:28.9 occ:1.00 O A:TYR193 2.5 23.8 1.0 O A:HOH546 2.6 38.1 1.0 O A:ILE197 2.6 34.6 1.0 O A:THR194 2.6 30.8 1.0 OD1 A:ASP200 2.7 29.3 1.0 O A:HOH573 2.8 35.3 1.0 OG1 A:THR194 2.8 32.3 1.0 C A:THR194 3.4 30.0 1.0 C A:TYR193 3.5 27.6 1.0 CB A:THR194 3.6 32.4 1.0 CG A:ASP200 3.7 26.0 1.0 C A:ILE197 3.8 42.2 1.0 OD2 A:ASP200 3.8 29.9 1.0 CA A:THR194 3.9 27.1 1.0 N A:THR194 4.0 25.1 1.0 CB A:ILE197 4.2 46.0 1.0 N A:ILE197 4.3 42.4 1.0 CA A:ILE197 4.4 42.1 1.0 N A:PRO195 4.4 29.6 1.0 O A:ASP200 4.5 26.0 1.0 N A:ASP200 4.6 31.6 1.0 CA A:TYR193 4.7 23.6 1.0 CA A:SER198 4.7 41.7 1.0 CD2 A:TYR193 4.7 27.6 1.0 CB A:TYR193 4.7 23.5 1.0 N A:SER198 4.7 40.6 1.0 O A:GLU190 4.8 24.2 1.0 CA A:PRO195 4.8 34.4 1.0 O A:HOH613 4.8 51.6 1.0 C A:ASP200 4.9 26.0 1.0 CG2 A:ILE197 4.9 41.1 1.0 CB A:ASP200 4.9 26.5 1.0 C A:SER198 4.9 40.2 1.0 CG2 A:THR194 5.0 28.1 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