Calcium in PDB 1fju: Thermolysin (80% Acetonitrile Soaked Crystals)

All present enzymatic activity of Thermolysin (80% Acetonitrile Soaked Crystals):
3.4.24.27;

The structure of Thermolysin (80% Acetonitrile Soaked Crystals), PDB code: 1fju 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 (°)	93.860, 93.860, 131.040, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 20.5

The structure of Thermolysin (80% Acetonitrile Soaked Crystals) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (80% Acetonitrile Soaked Crystals) (pdb code 1fju). 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 (80% Acetonitrile Soaked Crystals), PDB code: 1fju:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (80% Acetonitrile Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (80% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:22.6 occ:1.00 O A:HOH520 2.6 18.9 1.0 O A:GLU187 2.6 17.5 1.0 OD2 A:ASP138 2.6 21.9 1.0 OE1 A:GLU190 2.6 17.6 1.0 OE1 A:GLU177 2.6 21.6 1.0 OD1 A:ASP185 2.6 20.4 1.0 OE2 A:GLU190 2.7 18.1 1.0 OE2 A:GLU177 2.9 19.8 1.0 CD A:GLU190 3.1 27.9 1.0 CD A:GLU177 3.2 26.2 1.0 CG A:ASP138 3.5 24.4 1.0 CG A:ASP185 3.6 33.3 1.0 C A:GLU187 3.6 20.8 1.0 CA A:CA503 3.7 24.3 1.0 OD2 A:ASP185 3.8 18.9 1.0 CB A:ASP138 4.0 17.4 1.0 N A:GLU187 4.2 23.1 1.0 CA A:ILE188 4.3 17.9 1.0 O A:ASP185 4.3 24.7 1.0 OD1 A:ASP138 4.3 23.1 1.0 N A:GLY189 4.4 20.9 1.0 N A:ILE188 4.4 19.4 1.0 CA A:GLU187 4.4 20.0 1.0 O A:HOH648 4.4 47.2 1.0 CG A:GLU190 4.5 20.4 1.0 CG A:GLU177 4.6 18.7 1.0 CB A:GLU187 4.6 18.3 1.0 O A:HOH535 4.7 27.4 1.0 C A:ASP185 4.7 23.8 1.0 C A:ILE188 4.7 22.7 1.0 N A:ASP185 4.7 19.4 1.0 O A:HOH536 4.8 26.8 1.0 N A:GLU190 4.9 17.6 1.0 CB A:ASP185 4.9 19.4 1.0

Calcium binding site 2 out of 4 in the Thermolysin (80% Acetonitrile Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (80% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:24.3 occ:1.00 O A:HOH536 2.4 26.8 1.0 OD2 A:ASP185 2.5 18.9 1.0 OE2 A:GLU190 2.5 18.1 1.0 OE2 A:GLU177 2.5 19.8 1.0 O A:HOH519 2.6 23.0 1.0 O A:ASN183 2.6 23.8 1.0 CD A:GLU177 3.3 26.2 1.0 CG A:ASP185 3.4 33.3 1.0 CD A:GLU190 3.4 27.9 1.0 OD1 A:ASP185 3.7 20.4 1.0 OE1 A:GLU177 3.7 21.6 1.0 CA A:CA502 3.7 22.6 1.0 C A:ASN183 3.8 27.4 1.0 O A:LYS182 3.9 32.3 1.0 CG A:GLU190 4.0 20.4 1.0 N A:ASP185 4.1 19.4 1.0 CA A:PRO184 4.2 25.4 1.0 C A:PRO184 4.2 27.3 1.0 OE1 A:GLU190 4.3 17.6 1.0 OD2 A:ASP191 4.3 24.8 1.0 OD1 A:ASP191 4.3 23.5 1.0 CG A:GLU177 4.4 18.7 1.0 CB A:ASN183 4.4 35.3 1.0 CB A:ASP185 4.4 19.4 1.0 N A:PRO184 4.4 27.1 1.0 CG A:ASP191 4.7 26.9 1.0 CA A:ASN183 4.8 27.6 1.0 O A:HOH648 4.8 47.2 1.0 CA A:ASP185 4.9 21.6 1.0 O A:PRO184 4.9 23.4 1.0

Calcium binding site 3 out of 4 in the Thermolysin (80% Acetonitrile Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (80% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:22.6 occ:1.00 O A:GLN61 2.3 20.8 1.0 O A:HOH522 2.4 26.2 1.0 OD1 A:ASP59 2.6 23.2 1.0 O A:HOH533 2.6 20.2 1.0 OD1 A:ASP57 2.6 19.6 1.0 O A:HOH553 2.6 25.8 1.0 OD2 A:ASP57 2.7 19.8 1.0 CG A:ASP57 3.1 23.7 1.0 C A:GLN61 3.4 23.7 1.0 CG A:ASP59 3.5 30.9 1.0 OD2 A:ASP59 3.8 26.7 1.0 O A:HOH558 3.9 36.7 1.0 N A:GLN61 3.9 21.5 1.0 CA A:GLN61 4.1 24.5 1.0 N A:ASP59 4.3 20.0 1.0 CB A:GLN61 4.3 25.1 1.0 N A:PHE62 4.5 19.4 1.0 CB A:ASP57 4.5 19.0 1.0 N A:ASN60 4.6 21.1 1.0 O A:HOH515 4.6 18.2 1.0 OD2 A:ASP67 4.6 20.3 1.0 O A:HOH606 4.6 43.3 1.0 O A:HOH550 4.7 27.8 1.0 CA A:PHE62 4.7 19.9 1.0 CB A:ASP59 4.7 19.7 1.0 N A:ALA58 4.8 19.3 1.0 CA A:ASP59 4.8 20.4 1.0 C A:ASP59 4.9 20.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin (80% Acetonitrile Soaked Crystals)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (80% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:27.4 occ:1.00 O A:TYR193 2.5 22.2 1.0 O A:HOH544 2.6 39.1 1.0 OD1 A:ASP200 2.6 23.3 1.0 OG1 A:THR194 2.6 27.0 1.0 O A:THR194 2.6 25.8 1.0 O A:ILE197 2.6 34.2 1.0 O A:HOH570 2.8 29.4 1.0 C A:THR194 3.4 25.7 1.0 C A:TYR193 3.5 25.7 1.0 CG A:ASP200 3.6 24.2 1.0 CB A:THR194 3.7 27.3 1.0 OD2 A:ASP200 3.8 24.8 1.0 C A:ILE197 3.8 41.1 1.0 CA A:THR194 3.9 24.3 1.0 N A:THR194 4.1 22.6 1.0 N A:ILE197 4.2 42.9 1.0 CB A:ILE197 4.2 40.7 1.0 CA A:ILE197 4.3 40.0 1.0 N A:PRO195 4.4 28.3 1.0 O A:ASP200 4.6 23.7 1.0 N A:ASP200 4.6 25.9 1.0 CA A:TYR193 4.6 23.3 1.0 CB A:TYR193 4.6 24.4 1.0 CD2 A:TYR193 4.7 28.2 1.0 O A:GLU190 4.7 20.5 1.0 CA A:SER198 4.8 39.3 1.0 N A:SER198 4.8 38.6 1.0 CA A:PRO195 4.8 31.1 1.0 C A:ASP200 4.9 23.9 1.0 CB A:ASP200 4.9 23.7 1.0 C A:SER198 4.9 37.2 1.0 CG2 A:ILE197 5.0 37.9 1.0 CG2 A:THR194 5.0 24.6 1.0 CA A:ASP200 5.0 24.5 1.0 CG A:TYR193 5.0 24.6 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