Calcium in PDB 1fjv: Thermolysin (60% Acetonitrile Soaked Crystals)

All present enzymatic activity of Thermolysin (60% Acetonitrile Soaked Crystals):
3.4.24.27;

The structure of Thermolysin (60% Acetonitrile Soaked Crystals), PDB code: 1fjv 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 (°)	93.973, 93.973, 131.122, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 20.6

The structure of Thermolysin (60% Acetonitrile Soaked Crystals) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (60% Acetonitrile Soaked Crystals) (pdb code 1fjv). 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 (60% Acetonitrile Soaked Crystals), PDB code: 1fjv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (60% 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 (60% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:21.8 occ:1.00 OD2 A:ASP138 2.5 19.5 1.0 O A:GLU187 2.6 17.4 1.0 OE1 A:GLU190 2.6 17.2 1.0 OD1 A:ASP185 2.6 18.4 1.0 OE1 A:GLU177 2.7 19.7 1.0 OE2 A:GLU190 2.7 17.0 1.0 O A:HOH519 2.7 20.6 1.0 OE2 A:GLU177 2.9 16.5 1.0 CD A:GLU190 3.1 23.9 1.0 CD A:GLU177 3.2 22.2 1.0 CG A:ASP138 3.5 27.1 1.0 C A:GLU187 3.6 20.4 1.0 CG A:ASP185 3.6 28.8 1.0 CA A:CA503 3.8 23.9 1.0 OD2 A:ASP185 3.9 18.6 1.0 CB A:ASP138 4.0 18.6 1.0 N A:GLU187 4.2 21.4 1.0 O A:ASP185 4.3 20.4 1.0 CA A:ILE188 4.3 17.1 1.0 OD1 A:ASP138 4.3 20.0 1.0 N A:ILE188 4.4 17.4 1.0 CA A:GLU187 4.4 19.7 1.0 O A:HOH650 4.5 41.8 1.0 N A:GLY189 4.5 20.4 1.0 CG A:GLU190 4.5 19.5 1.0 O A:HOH534 4.6 25.1 1.0 CG A:GLU177 4.6 16.5 1.0 CB A:GLU187 4.6 24.9 1.0 C A:ASP185 4.7 22.8 1.0 N A:ASP185 4.8 19.4 1.0 C A:ILE188 4.8 20.0 1.0 N A:GLU190 4.9 17.0 1.0 CB A:ASP185 4.9 20.5 1.0 O A:HOH535 5.0 30.0 1.0 CB A:GLU177 5.0 17.2 1.0

Calcium binding site 2 out of 4 in the Thermolysin (60% 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 (60% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:23.9 occ:1.00 O A:HOH535 2.5 30.0 1.0 OE2 A:GLU177 2.5 16.5 1.0 OD2 A:ASP185 2.5 18.6 1.0 OE2 A:GLU190 2.5 17.0 1.0 O A:HOH518 2.5 23.5 1.0 O A:ASN183 2.6 25.6 1.0 CD A:GLU177 3.3 22.2 1.0 CG A:ASP185 3.4 28.8 1.0 CD A:GLU190 3.4 23.9 1.0 OD1 A:ASP185 3.6 18.4 1.0 C A:ASN183 3.7 29.2 1.0 CA A:CA502 3.8 21.8 1.0 OE1 A:GLU177 3.8 19.7 1.0 O A:LYS182 3.9 30.3 1.0 CG A:GLU190 4.0 19.5 1.0 N A:ASP185 4.2 19.4 1.0 CA A:PRO184 4.2 24.6 1.0 C A:PRO184 4.2 26.0 1.0 OE1 A:GLU190 4.3 17.2 1.0 OD1 A:ASP191 4.3 22.4 1.0 CG A:GLU177 4.3 16.5 1.0 OD2 A:ASP191 4.4 23.2 1.0 CB A:ASN183 4.4 35.0 1.0 N A:PRO184 4.4 28.5 1.0 CB A:ASP185 4.5 20.5 1.0 CG A:ASP191 4.7 25.3 1.0 O A:HOH650 4.7 41.8 1.0 CA A:ASN183 4.7 28.7 1.0 O A:PRO184 4.9 20.9 1.0 CA A:ASP185 4.9 22.1 1.0 C A:LYS182 5.0 30.7 1.0

Calcium binding site 3 out of 4 in the Thermolysin (60% 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 (60% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:21.9 occ:1.00 O A:GLN61 2.5 19.5 1.0 O A:HOH532 2.5 20.6 1.0 OD1 A:ASP59 2.6 19.9 1.0 OD1 A:ASP57 2.6 20.8 1.0 O A:HOH521 2.6 33.9 1.0 OD2 A:ASP57 2.7 18.6 1.0 O A:HOH552 2.7 26.1 1.0 CG A:ASP57 3.1 24.0 1.0 CG A:ASP59 3.5 29.7 1.0 C A:GLN61 3.7 24.3 1.0 OD2 A:ASP59 3.8 24.5 1.0 N A:GLN61 3.9 20.7 1.0 O A:HOH557 4.0 35.8 1.0 CA A:GLN61 4.3 22.9 1.0 N A:ASP59 4.3 21.8 1.0 CB A:GLN61 4.4 25.4 1.0 CB A:ASP57 4.5 17.1 1.0 O A:HOH605 4.6 64.5 1.0 N A:PHE62 4.6 19.6 1.0 N A:ASN60 4.6 21.4 1.0 O A:HOH549 4.6 25.4 1.0 CA A:PHE62 4.7 19.4 1.0 OD2 A:ASP67 4.7 19.4 1.0 O A:HOH514 4.7 21.0 1.0 CB A:ASP59 4.7 22.4 1.0 N A:ALA58 4.8 18.7 1.0 CA A:ASP59 4.8 22.0 1.0 C A:ASP59 4.9 23.1 1.0

Calcium binding site 4 out of 4 in the Thermolysin (60% 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 (60% Acetonitrile Soaked Crystals) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:26.6 occ:1.00 O A:TYR193 2.6 19.0 1.0 O A:HOH570 2.6 25.3 1.0 OD1 A:ASP200 2.6 23.6 1.0 O A:THR194 2.6 26.3 1.0 O A:ILE197 2.6 31.9 1.0 O A:HOH543 2.7 48.5 1.0 OG1 A:THR194 2.7 28.4 1.0 C A:THR194 3.4 27.2 1.0 C A:TYR193 3.6 25.5 1.0 CG A:ASP200 3.6 21.6 1.0 CB A:THR194 3.7 30.4 1.0 OD2 A:ASP200 3.8 24.8 1.0 CA A:THR194 3.8 24.1 1.0 C A:ILE197 3.8 38.9 1.0 N A:THR194 4.0 23.1 1.0 N A:ILE197 4.2 39.2 1.0 CB A:ILE197 4.2 41.4 1.0 CA A:ILE197 4.3 39.6 1.0 N A:PRO195 4.4 26.2 1.0 O A:ASP200 4.6 24.6 1.0 N A:ASP200 4.6 27.1 1.0 O A:GLU190 4.7 21.7 1.0 CA A:TYR193 4.7 21.1 1.0 CD2 A:TYR193 4.7 26.8 1.0 CA A:SER198 4.7 38.0 1.0 N A:SER198 4.7 38.9 1.0 CB A:TYR193 4.8 24.7 1.0 CG2 A:ILE197 4.8 38.6 1.0 CA A:PRO195 4.8 31.4 1.0 C A:ASP200 4.9 22.5 1.0 CB A:ASP200 4.9 27.3 1.0 O A:HOH610 4.9 42.0 1.0 CG2 A:THR194 5.0 28.0 1.0 C A:SER198 5.0 35.8 1.0 C A:PRO195 5.0 36.0 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