Calcium in PDB 3fbo: Metal Exchange in Thermolysin

All present enzymatic activity of Metal Exchange in Thermolysin:
3.4.24.27;

The structure of Metal Exchange in Thermolysin, PDB code: 3fbo was solved by L.Englert, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.92
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.962, 92.962, 127.489, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 26

The structure of Metal Exchange in Thermolysin also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Calcium atom in the Metal Exchange in Thermolysin (pdb code 3fbo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Metal Exchange in Thermolysin, PDB code: 3fbo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metal Exchange in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3000 b:24.6 occ:1.00 OD2 A:ASP138 2.3 28.6 1.0 O A:GLU187 2.4 25.1 1.0 OE1 A:GLU177 2.4 24.8 1.0 O A:HOH3106 2.4 23.4 1.0 OE2 A:GLU190 2.4 21.0 1.0 OD1 A:ASP185 2.5 20.0 1.0 OE1 A:GLU190 2.6 22.0 1.0 CD A:GLU190 2.9 19.5 1.0 OE2 A:GLU177 2.9 25.0 1.0 CD A:GLU177 3.0 23.4 1.0 CG A:ASP138 3.4 26.6 1.0 CG A:ASP185 3.5 23.3 1.0 C A:GLU187 3.5 23.9 1.0 OD2 A:ASP185 3.8 26.5 1.0 CA A:CA3001 3.8 23.4 1.0 CB A:ASP138 4.0 22.0 1.0 O A:ASP185 4.2 26.4 1.0 N A:GLU187 4.2 18.9 1.0 OD1 A:ASP138 4.3 24.8 1.0 O A:HOH3182 4.3 38.5 1.0 CA A:ILE188 4.3 24.7 1.0 CG A:GLU190 4.4 22.2 1.0 N A:ILE188 4.4 25.5 1.0 N A:GLY189 4.4 21.4 1.0 CA A:GLU187 4.4 22.8 1.0 CG A:GLU177 4.5 20.7 1.0 O A:HOH3170 4.5 27.0 1.0 C A:ASP185 4.6 29.0 1.0 CB A:ASP185 4.7 24.2 1.0 CB A:GLU187 4.8 27.6 1.0 C A:ILE188 4.8 28.8 1.0 N A:ASP185 4.8 21.4 1.0 CB A:GLU177 4.9 24.7 1.0 N A:GLU190 4.9 25.3 1.0 CA A:ASP185 5.0 26.2 1.0 O A:HOH3105 5.0 26.1 1.0

Calcium binding site 2 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metal Exchange in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:23.4 occ:1.00 OD2 A:ASP185 2.2 26.5 1.0 O A:HOH3104 2.2 32.5 1.0 OE2 A:GLU190 2.3 21.0 1.0 O A:ASN183 2.3 25.5 1.0 O A:HOH3105 2.3 26.1 1.0 OE2 A:GLU177 2.4 25.0 1.0 CG A:ASP185 3.1 23.3 1.0 CD A:GLU177 3.3 23.4 1.0 CD A:GLU190 3.3 19.5 1.0 C A:ASN183 3.5 21.7 1.0 OD1 A:ASP185 3.6 20.0 1.0 CG A:GLU190 3.8 22.2 1.0 OE1 A:GLU177 3.8 24.8 1.0 CA A:CA3000 3.8 24.6 1.0 OD2 A:ASP191 4.0 29.9 1.0 CA A:PRO184 4.1 25.8 1.0 OD1 A:ASP191 4.2 27.6 1.0 C A:PRO184 4.2 32.5 1.0 N A:ASP185 4.2 21.4 1.0 O A:LYS182 4.2 33.2 1.0 CG A:GLU177 4.3 20.7 1.0 CB A:ASN183 4.3 33.5 1.0 N A:PRO184 4.3 21.1 1.0 CB A:ASP185 4.3 24.2 1.0 OE1 A:GLU190 4.4 22.0 1.0 O A:HOH3182 4.4 38.5 1.0 CG A:ASP191 4.4 29.1 1.0 CA A:ASN183 4.5 29.1 1.0 O A:HOH3205 4.7 45.6 1.0 O A:PRO184 4.8 31.0 1.0 CA A:ASP185 4.9 26.2 1.0

Calcium binding site 3 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metal Exchange in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3002 b:24.3 occ:1.00 O A:GLN61 2.3 15.5 1.0 OD2 A:ASP57 2.3 19.1 1.0 O A:HOH3102 2.4 22.7 1.0 OD1 A:ASP59 2.4 23.6 1.0 O A:HOH3103 2.4 23.4 1.0 O A:HOH3101 2.5 24.8 1.0 OD1 A:ASP57 2.5 21.6 1.0 CG A:ASP57 2.8 29.1 1.0 CG A:ASP59 3.4 28.0 1.0 C A:GLN61 3.5 16.1 1.0 OD2 A:ASP59 3.8 29.5 1.0 N A:GLN61 4.0 27.3 1.0 O A:HOH3140 4.0 21.8 1.0 O A:HOH3193 4.1 40.3 1.0 CA A:GLN61 4.2 23.1 1.0 CB A:ASP57 4.3 22.7 1.0 N A:ASP59 4.3 31.4 1.0 O A:HOH3147 4.4 23.8 1.0 CB A:GLN61 4.4 25.9 1.0 N A:PHE62 4.6 18.5 1.0 OD2 A:ASP67 4.6 22.8 1.0 O A:HOH3132 4.7 26.2 1.0 CB A:ASP59 4.7 28.7 1.0 CA A:PHE62 4.7 17.9 1.0 N A:ASN60 4.7 19.4 1.0 N A:ALA58 4.8 22.8 1.0 CA A:ASP59 4.9 23.8 1.0 C A:ASP59 4.9 25.7 1.0

Calcium binding site 4 out of 4 in the Metal Exchange in Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Metal Exchange in Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3003 b:28.1 occ:1.00 O A:TYR193 2.2 21.9 1.0 O A:HOH3108 2.3 30.6 1.0 O A:ILE197 2.3 33.0 1.0 O A:THR194 2.3 29.9 1.0 OG1 A:THR194 2.4 28.9 1.0 O A:HOH3107 2.5 28.6 1.0 OD1 A:ASP200 2.6 27.9 1.0 C A:THR194 3.2 24.7 1.0 C A:TYR193 3.2 25.5 1.0 C A:ILE197 3.4 39.4 1.0 CB A:THR194 3.5 31.6 1.0 CG A:ASP200 3.6 27.6 1.0 CA A:THR194 3.7 29.2 1.0 N A:THR194 3.8 30.2 1.0 OD2 A:ASP200 3.9 31.4 1.0 N A:ILE197 4.1 42.4 1.0 CA A:ILE197 4.1 29.0 1.0 N A:PRO195 4.3 26.7 1.0 CB A:ILE197 4.4 31.0 1.0 CA A:TYR193 4.4 23.8 1.0 N A:SER198 4.5 30.9 1.0 CB A:TYR193 4.6 25.0 1.0 O A:ASP200 4.6 31.7 1.0 N A:ASP200 4.6 27.7 1.0 CA A:PRO195 4.6 27.5 1.0 O A:GLU190 4.7 22.1 1.0 CG2 A:THR194 4.7 26.1 1.0 CD2 A:TYR193 4.7 30.4 1.0 CA A:SER198 4.8 30.3 1.0 C A:PRO195 4.9 40.7 1.0 N A:TYR193 4.9 24.5 1.0 CB A:ASP200 4.9 23.8 1.0 CG A:TYR193 5.0 23.8 1.0 C A:ASP200 5.0 24.3 1.0

L.Englert, A.Heine, G.Klebe. Metal Exchange in Thermolysin To Be Published.