Calcium in PDB 1pe5: Thermolysin with Tricyclic Inhibitor

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

The structure of Thermolysin with Tricyclic Inhibitor, PDB code: 1pe5 was solved by D.Juers, D.Holland, B.P.Morgan, 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 / 1.70
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 Tricyclic Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin with Tricyclic Inhibitor (pdb code 1pe5). 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 Tricyclic Inhibitor, PDB code: 1pe5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin with Tricyclic 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 Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:9.4 occ:1.00 O A:GLU187 2.3 8.0 1.0 OD1 A:ASP138 2.3 10.8 1.0 OE1 A:GLU190 2.4 10.9 1.0 OD2 A:ASP185 2.4 10.1 1.0 OE1 A:GLU177 2.5 12.3 1.0 OE2 A:GLU190 2.5 9.3 1.0 O A:HOH346 2.6 10.3 1.0 CD A:GLU190 2.8 12.9 1.0 OE2 A:GLU177 2.9 9.8 1.0 CD A:GLU177 3.0 11.1 1.0 CG A:ASP138 3.3 7.7 1.0 C A:GLU187 3.4 9.1 1.0 CG A:ASP185 3.5 14.1 1.0 OD1 A:ASP185 3.7 11.0 1.0 CA A:CA319 3.8 11.8 1.0 CB A:ASP138 4.0 6.4 1.0 N A:ILE188 4.2 9.9 1.0 CG A:GLU190 4.3 5.4 1.0 CA A:ILE188 4.3 6.2 1.0 N A:GLU187 4.3 17.2 1.0 OD2 A:ASP138 4.3 14.6 1.0 CA A:GLU187 4.3 11.1 1.0 O A:ASP185 4.3 15.9 1.0 N A:GLY189 4.4 15.5 1.0 O A:HOH469 4.4 38.2 1.0 CG A:GLU177 4.4 7.8 1.0 O A:HOH350 4.5 16.4 1.0 CB A:GLU187 4.6 10.4 1.0 C A:ASP185 4.7 20.2 1.0 C A:ILE188 4.7 16.9 1.0 CB A:ASP185 4.7 11.8 1.0 N A:ASP185 4.8 9.5 1.0 N A:GLU190 4.9 8.7 1.0 CB A:GLU177 4.9 3.0 1.0 O A:HOH353 5.0 15.3 1.0

Calcium binding site 2 out of 4 in the Thermolysin with Tricyclic 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 Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:11.8 occ:1.00 OD1 A:ASP185 2.3 11.0 1.0 OE2 A:GLU177 2.3 9.8 1.0 OE2 A:GLU190 2.3 9.3 1.0 O A:HOH475 2.3 14.1 1.0 O A:HOH353 2.4 15.3 1.0 O A:ASN183 2.4 15.4 1.0 CG A:ASP185 3.2 14.1 1.0 CD A:GLU177 3.3 11.1 1.0 CD A:GLU190 3.3 12.9 1.0 C A:ASN183 3.6 6.9 1.0 OD2 A:ASP185 3.6 10.1 1.0 CG A:GLU190 3.7 5.4 1.0 OE1 A:GLU177 3.8 12.3 1.0 CA A:CA318 3.8 9.4 1.0 O A:LYS182 3.9 24.1 1.0 CA A:PRO184 4.1 14.2 1.0 N A:ASP185 4.1 9.5 1.0 CB A:ASN183 4.2 12.6 1.0 C A:PRO184 4.2 28.3 1.0 CG A:GLU177 4.2 7.8 1.0 OE1 A:GLU190 4.3 10.9 1.0 N A:PRO184 4.3 17.1 1.0 OD1 A:ASP191 4.3 13.9 1.0 OD2 A:ASP191 4.4 14.3 1.0 CB A:ASP185 4.4 11.8 1.0 CA A:ASN183 4.7 8.1 1.0 CG A:ASP191 4.7 20.7 1.0 O A:HOH469 4.8 38.2 1.0 O A:PRO184 4.9 17.5 1.0 CA A:ASP185 4.9 9.2 1.0

Calcium binding site 3 out of 4 in the Thermolysin with Tricyclic 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 Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:11.3 occ:1.00 O A:GLN61 2.2 10.9 1.0 O A:HOH503 2.4 14.4 1.0 OD1 A:ASP57 2.4 11.9 1.0 OD1 A:ASP59 2.4 13.1 1.0 O A:HOH482 2.4 16.3 1.0 O A:HOH419 2.5 13.7 1.0 OD2 A:ASP57 2.5 12.2 1.0 CG A:ASP57 2.8 9.4 1.0 CG A:ASP59 3.4 21.9 1.0 C A:GLN61 3.4 12.4 1.0 OD2 A:ASP59 3.7 17.0 1.0 N A:GLN61 4.0 7.9 1.0 O A:HOH484 4.0 23.9 1.0 CA A:GLN61 4.2 8.6 1.0 N A:ASP59 4.2 13.4 1.0 CB A:GLN61 4.3 8.8 1.0 CB A:ASP57 4.3 4.0 1.0 N A:PHE62 4.5 7.0 1.0 O A:HOH508 4.5 13.0 1.0 OD2 A:ASP67 4.6 6.4 1.0 O A:HOH356 4.6 11.8 1.0 CA A:PHE62 4.7 12.7 1.0 CB A:ASP59 4.7 12.8 1.0 N A:ALA58 4.7 8.6 1.0 N A:ASN60 4.8 14.7 1.0 CA A:ASP59 4.9 9.5 1.0 C A:ASP59 4.9 19.0 1.0

Calcium binding site 4 out of 4 in the Thermolysin with Tricyclic 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 Tricyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca321 b:14.6 occ:1.00 O A:HOH480 2.1 30.0 1.0 O A:ILE197 2.2 32.1 1.0 OD1 A:ASP200 2.2 14.8 1.0 OG1 A:THR194 2.2 16.6 1.0 O A:THR194 2.4 17.2 1.0 O A:TYR193 2.4 12.1 1.0 O A:HOH354 2.4 14.6 1.0 C A:THR194 3.2 16.4 1.0 CG A:ASP200 3.3 12.1 1.0 C A:ILE197 3.4 32.8 1.0 CB A:THR194 3.4 15.4 1.0 C A:TYR193 3.4 19.8 1.0 OD2 A:ASP200 3.7 15.7 1.0 CA A:THR194 3.7 10.9 1.0 N A:THR194 4.0 15.9 1.0 CA A:ILE197 4.1 17.5 1.0 N A:ILE197 4.2 43.8 1.0 CB A:ILE197 4.2 25.5 1.0 N A:PRO195 4.2 17.1 1.0 N A:SER198 4.4 28.7 1.0 O A:ASP200 4.5 16.6 1.0 CA A:SER198 4.5 34.5 1.0 N A:ASP200 4.5 16.1 1.0 CG2 A:THR194 4.6 13.9 1.0 O A:GLU190 4.6 14.0 1.0 CB A:ASP200 4.6 12.4 1.0 CA A:TYR193 4.6 12.8 1.0 CD2 A:TYR193 4.7 17.7 1.0 CA A:PRO195 4.7 17.5 1.0 O A:HOH476 4.7 31.9 1.0 C A:ASP200 4.8 14.0 1.0 CG2 A:ILE197 4.8 19.7 1.0 C A:SER198 4.8 23.5 1.0 CB A:TYR193 4.8 14.7 1.0 CA A:ASP200 4.9 14.5 1.0 N A:GLY199 4.9 20.9 1.0 C A:PRO195 5.0 37.7 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.