Calcium in PDB 1pe7: Thermolysin with Bicyclic Inhibitor

All present enzymatic activity of Thermolysin with Bicyclic Inhibitor:
3.4.24.27;

The structure of Thermolysin with Bicyclic Inhibitor, PDB code: 1pe7 was solved by D.Juers, N.Yusuff, P.A.Bartlett, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.82
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.800, 93.800, 131.400, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of Thermolysin with Bicyclic Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin with Bicyclic Inhibitor (pdb code 1pe7). 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 with Bicyclic Inhibitor, PDB code: 1pe7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin with Bicyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin with Bicyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:16.2 occ:1.00 O A:GLU187 2.3 13.0 1.0 OD2 A:ASP138 2.3 16.5 1.0 OE1 A:GLU190 2.4 15.3 1.0 OD1 A:ASP185 2.4 19.2 1.0 OE1 A:GLU177 2.5 17.3 1.0 OE2 A:GLU190 2.6 13.8 1.0 O A:HOH346 2.6 14.4 1.0 CD A:GLU190 2.8 15.3 1.0 OE2 A:GLU177 2.9 16.5 1.0 CD A:GLU177 3.0 19.6 1.0 CG A:ASP185 3.3 24.7 1.0 C A:GLU187 3.4 16.8 1.0 CG A:ASP138 3.4 16.6 1.0 OD2 A:ASP185 3.7 17.0 1.0 CA A:CA319 3.8 17.8 1.0 CB A:ASP138 4.0 9.4 1.0 N A:GLU187 4.1 19.1 1.0 N A:ILE188 4.2 13.9 1.0 CG A:GLU190 4.3 14.3 1.0 OD1 A:ASP138 4.3 18.7 1.0 CA A:ILE188 4.3 12.7 1.0 CA A:GLU187 4.3 16.1 1.0 O A:ASP185 4.3 21.9 1.0 N A:GLY189 4.4 18.2 1.0 CG A:GLU177 4.4 18.1 1.0 O A:HOH350 4.5 23.6 1.0 CB A:GLU187 4.5 15.9 1.0 C A:ASP185 4.7 18.3 1.0 CB A:ASP185 4.7 17.4 1.0 C A:ILE188 4.7 15.2 1.0 N A:ASP185 4.8 16.4 1.0 N A:GLU190 4.9 15.9 1.0 O A:HOH353 4.9 20.3 1.0 CB A:GLU177 5.0 15.1 1.0

Calcium binding site 2 out of 4 in the Thermolysin with Bicyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin with Bicyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:17.8 occ:1.00 OE2 A:GLU190 2.3 13.8 1.0 OE2 A:GLU177 2.3 16.5 1.0 O A:HOH353 2.3 20.3 1.0 OD2 A:ASP185 2.4 17.0 1.0 O A:ASN183 2.4 21.5 1.0 O A:HOH475 2.4 21.9 1.0 CD A:GLU177 3.2 19.6 1.0 CG A:ASP185 3.3 24.7 1.0 CD A:GLU190 3.4 15.3 1.0 C A:ASN183 3.6 14.2 1.0 OE1 A:GLU177 3.7 17.3 1.0 OD1 A:ASP185 3.8 19.2 1.0 CG A:GLU190 3.8 14.3 1.0 CA A:CA318 3.8 16.2 1.0 O A:LYS182 3.9 29.8 1.0 N A:ASP185 4.1 16.4 1.0 CA A:PRO184 4.1 23.1 1.0 CB A:ASN183 4.1 19.5 1.0 OD2 A:ASP191 4.2 17.5 1.0 CG A:GLU177 4.2 18.1 1.0 C A:PRO184 4.3 34.1 1.0 OE1 A:GLU190 4.3 15.3 1.0 N A:PRO184 4.3 24.9 1.0 OD1 A:ASP191 4.3 19.2 1.0 CB A:ASP185 4.5 17.4 1.0 CG A:ASP191 4.6 26.2 1.0 CA A:ASN183 4.6 19.8 1.0 CA A:ASP185 4.9 17.2 1.0 O A:PRO184 5.0 21.0 1.0

Calcium binding site 3 out of 4 in the Thermolysin with Bicyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin with Bicyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:16.0 occ:1.00 O A:GLN61 2.2 17.4 1.0 O A:HOH503 2.3 18.2 1.0 O A:HOH482 2.3 24.9 1.0 OD1 A:ASP59 2.4 19.7 1.0 O A:HOH419 2.4 17.1 1.0 OD1 A:ASP57 2.4 17.9 1.0 OD2 A:ASP57 2.5 14.4 1.0 CG A:ASP57 2.8 17.9 1.0 CG A:ASP59 3.4 29.9 1.0 C A:GLN61 3.5 19.5 1.0 OD2 A:ASP59 3.7 20.3 1.0 O A:HOH484 3.9 32.8 1.0 N A:GLN61 4.0 14.5 1.0 CA A:GLN61 4.2 16.7 1.0 N A:ASP59 4.3 16.1 1.0 CB A:ASP57 4.3 8.6 1.0 CB A:GLN61 4.3 12.7 1.0 O A:HOH628 4.4 41.6 1.0 O A:HOH508 4.4 22.9 1.0 N A:PHE62 4.5 15.3 1.0 O A:HOH356 4.6 14.0 1.0 OD2 A:ASP67 4.6 15.8 1.0 CA A:PHE62 4.7 13.8 1.0 N A:ALA58 4.7 12.4 1.0 N A:ASN60 4.7 15.8 1.0 CB A:ASP59 4.7 17.6 1.0 CA A:ASP59 4.8 15.3 1.0 C A:ASP59 4.9 19.4 1.0

Calcium binding site 4 out of 4 in the Thermolysin with Bicyclic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin with Bicyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca321 b:23.1 occ:1.00 O A:ILE197 2.2 39.6 1.0 OG1 A:THR194 2.2 20.4 1.0 OD1 A:ASP200 2.3 21.3 1.0 O A:THR194 2.3 19.0 1.0 O A:HOH480 2.3 29.5 1.0 O A:TYR193 2.4 16.9 1.0 O A:HOH354 2.4 20.0 1.0 C A:THR194 3.1 39.0 1.0 CG A:ASP200 3.3 16.3 1.0 C A:TYR193 3.4 25.4 1.0 CB A:THR194 3.4 19.2 1.0 C A:ILE197 3.4 48.2 1.0 CA A:THR194 3.6 26.4 1.0 OD2 A:ASP200 3.7 24.6 1.0 N A:THR194 3.9 23.8 1.0 N A:PRO195 4.1 23.2 1.0 CA A:ILE197 4.2 35.5 1.0 CB A:ILE197 4.2 39.2 1.0 N A:ILE197 4.2 48.9 1.0 O A:ASP200 4.4 20.2 1.0 N A:SER198 4.4 33.5 1.0 O A:GLU190 4.5 18.2 1.0 CA A:SER198 4.6 39.3 1.0 N A:ASP200 4.6 24.2 1.0 CA A:PRO195 4.6 33.7 1.0 CA A:TYR193 4.6 17.8 1.0 CD2 A:TYR193 4.6 20.2 1.0 CB A:ASP200 4.6 19.4 1.0 CG2 A:THR194 4.6 19.5 1.0 CB A:TYR193 4.7 19.0 1.0 O A:HOH476 4.8 44.0 1.0 C A:ASP200 4.8 17.6 1.0 C A:PRO195 4.9 51.3 1.0 CA A:ASP200 4.9 19.5 1.0 CG A:TYR193 4.9 25.8 1.0 C A:SER198 4.9 34.4 1.0 CG2 A:ILE197 5.0 23.2 1.0

P.A.Bartlett, N.Yusuff, M.K.Lindval, D.Holland, D.Juers, B.W.Matthews. Conformational Constraint and Structural Complementarity in Thermolysin Inhibitors: Structures of Enzyme Complexes and Conclusions To Be Published.