Calcium in PDB 1kei: Thermolysin (Substrate-Free)

All present enzymatic activity of Thermolysin (Substrate-Free):
3.4.24.27;

The structure of Thermolysin (Substrate-Free), PDB code: 1kei was solved by M.Senda, T.Senda, S.Kidokoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.48 / 1.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.541, 93.541, 131.141, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 18.8

The structure of Thermolysin (Substrate-Free) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin (Substrate-Free) (pdb code 1kei). 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 (Substrate-Free), PDB code: 1kei:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin (Substrate-Free)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin (Substrate-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:13.2 occ:1.00 O A:GLU187 2.3 14.2 1.0 OD2 A:ASP138 2.4 13.3 1.0 O A:HOH1005 2.5 13.5 1.0 OE1 A:GLU177 2.5 12.9 1.0 OD1 A:ASP185 2.5 14.4 1.0 OE1 A:GLU190 2.5 13.0 1.0 OE2 A:GLU190 2.5 14.2 1.0 OE2 A:GLU177 2.8 14.1 1.0 CD A:GLU190 2.8 13.6 1.0 CD A:GLU177 3.0 14.3 1.0 CG A:ASP138 3.4 14.0 1.0 C A:GLU187 3.4 14.3 1.0 CG A:ASP185 3.5 16.2 1.0 CA A:CA402 3.8 15.2 1.0 OD2 A:ASP185 3.9 17.2 1.0 CB A:ASP138 4.0 12.5 1.0 N A:GLU187 4.2 15.6 1.0 O A:ASP185 4.2 15.6 1.0 N A:ILE188 4.3 13.2 1.0 O A:HOH1143 4.3 34.4 1.0 CA A:ILE188 4.3 13.6 1.0 CA A:GLU187 4.3 16.0 1.0 OD1 A:ASP138 4.3 15.1 1.0 CG A:GLU190 4.3 13.6 1.0 CG A:GLU177 4.4 13.8 1.0 N A:GLY189 4.5 13.2 1.0 O A:HOH1043 4.5 18.4 1.0 CB A:GLU187 4.6 17.8 1.0 C A:ASP185 4.6 15.1 1.0 C A:ILE188 4.8 13.6 1.0 CB A:ASP185 4.8 15.5 1.0 N A:ASP185 4.8 15.7 1.0 O A:HOH1030 4.9 18.1 1.0 N A:GLU190 4.9 12.8 1.0 CB A:GLU177 4.9 13.2 1.0

Calcium binding site 2 out of 4 in the Thermolysin (Substrate-Free)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin (Substrate-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:15.2 occ:1.00 OE2 A:GLU190 2.3 14.2 1.0 O A:ASN183 2.3 18.9 1.0 OD2 A:ASP185 2.3 17.2 1.0 O A:HOH1019 2.4 17.8 1.0 OE2 A:GLU177 2.4 14.1 1.0 O A:HOH1030 2.4 18.1 1.0 CG A:ASP185 3.2 16.2 1.0 CD A:GLU177 3.3 14.3 1.0 CD A:GLU190 3.3 13.6 1.0 C A:ASN183 3.5 20.5 1.0 OD1 A:ASP185 3.6 14.4 1.0 CG A:GLU190 3.8 13.6 1.0 O A:LYS182 3.8 26.3 1.0 OE1 A:GLU177 3.8 12.9 1.0 CA A:CA401 3.8 13.2 1.0 CB A:ASN183 4.2 25.4 1.0 OD2 A:ASP191 4.2 18.5 1.0 N A:ASP185 4.2 15.7 1.0 OE1 A:GLU190 4.2 13.0 1.0 CA A:PRO184 4.2 18.9 1.0 CG A:GLU177 4.3 13.8 1.0 N A:PRO184 4.3 20.2 1.0 C A:PRO184 4.3 18.9 1.0 OD1 A:ASP191 4.3 18.8 1.0 CB A:ASP185 4.4 15.5 1.0 CA A:ASN183 4.5 23.0 1.0 CG A:ASP191 4.6 17.0 1.0 O A:HOH1143 4.6 34.4 1.0 C A:LYS182 4.9 25.7 1.0 CA A:ASP185 4.9 15.6 1.0 O A:PRO184 4.9 19.2 1.0

Calcium binding site 3 out of 4 in the Thermolysin (Substrate-Free)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin (Substrate-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:14.2 occ:1.00 O A:GLN61 2.3 14.4 1.0 O A:HOH1016 2.3 18.6 1.0 OD1 A:ASP59 2.4 16.6 1.0 OD1 A:ASP57 2.4 15.6 1.0 O A:HOH1014 2.4 15.1 1.0 O A:HOH1021 2.5 19.4 1.0 OD2 A:ASP57 2.5 16.0 1.0 CG A:ASP57 2.8 14.9 1.0 CG A:ASP59 3.4 17.8 1.0 C A:GLN61 3.5 13.8 1.0 OD2 A:ASP59 3.8 20.0 1.0 N A:GLN61 4.0 14.2 1.0 O A:HOH1055 4.1 25.6 1.0 CA A:GLN61 4.2 14.9 1.0 N A:ASP59 4.3 15.8 1.0 CB A:ASP57 4.3 13.7 1.0 CB A:GLN61 4.4 18.9 1.0 N A:PHE62 4.5 12.9 1.0 O A:HOH1133 4.6 38.5 1.0 O A:HOH1025 4.6 21.0 1.0 O A:HOH1003 4.6 14.0 1.0 CB A:ASP59 4.6 16.4 1.0 N A:ASN60 4.7 14.6 1.0 OD2 A:ASP67 4.7 14.2 1.0 CA A:PHE62 4.7 13.1 1.0 N A:ALA58 4.8 15.3 1.0 CA A:ASP59 4.8 16.0 1.0 C A:ASP59 4.9 15.4 1.0 O A:HOH1154 5.0 45.8 1.0

Calcium binding site 4 out of 4 in the Thermolysin (Substrate-Free)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin (Substrate-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:17.7 occ:1.00 O A:ILE197 2.1 28.9 1.0 O A:TYR193 2.3 16.5 1.0 O A:THR194 2.3 21.6 1.0 OG1 A:THR194 2.3 21.0 1.0 OD1 A:ASP200 2.4 20.0 1.0 O A:HOH1009 2.4 19.4 1.0 O A:HOH1051 2.5 29.3 1.0 C A:THR194 3.2 21.8 1.0 C A:ILE197 3.3 31.5 1.0 C A:TYR193 3.4 17.4 1.0 CG A:ASP200 3.4 19.3 1.0 CB A:THR194 3.4 19.9 1.0 CA A:THR194 3.7 19.6 1.0 OD2 A:ASP200 3.8 21.4 1.0 N A:THR194 3.9 17.7 1.0 CA A:ILE197 4.1 30.9 1.0 CB A:ILE197 4.2 31.9 1.0 N A:PRO195 4.2 23.0 1.0 N A:ILE197 4.2 31.4 1.0 N A:SER198 4.3 31.2 1.0 O A:ASP200 4.4 19.4 1.0 CA A:SER198 4.5 32.0 1.0 CA A:TYR193 4.6 17.0 1.0 O A:GLU190 4.6 15.8 1.0 CA A:PRO195 4.6 25.7 1.0 N A:ASP200 4.6 22.8 1.0 CG2 A:THR194 4.7 21.1 1.0 O A:HOH1067 4.7 35.0 1.0 CB A:ASP200 4.7 20.6 1.0 CB A:TYR193 4.8 18.0 1.0 CD2 A:TYR193 4.8 22.1 1.0 C A:ASP200 4.8 18.9 1.0 CG2 A:ILE197 4.9 31.1 1.0 C A:SER198 4.9 30.9 1.0 C A:PRO195 4.9 27.4 1.0 CA A:ASP200 5.0 20.1 1.0

M.Senda, T.Senda, S.Kidokoro. Crystal Structure Analyses of Thermolysin in Complex with Its Inhibitors To Be Published.