Calcium in PDB 1pe8: Thermolysin with Monocyclic Inhibitor

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

The structure of Thermolysin with Monocyclic Inhibitor, PDB code: 1pe8 was solved by D.Juers, H.-J.Pyun, 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 / 1.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.700, 93.700, 131.600, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

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

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin with Monocyclic Inhibitor (pdb code 1pe8). 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 Monocyclic Inhibitor, PDB code: 1pe8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin with Monocyclic 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 Monocyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:12.7 occ:1.00 O A:GLU187 2.3 10.7 1.0 OD2 A:ASP138 2.3 13.5 1.0 OE1 A:GLU177 2.4 13.5 1.0 OE1 A:GLU190 2.4 12.5 1.0 OD1 A:ASP185 2.5 13.1 1.0 OE2 A:GLU190 2.5 12.8 1.0 O A:HOH346 2.5 11.1 1.0 CD A:GLU190 2.8 10.6 1.0 OE2 A:GLU177 2.8 15.2 1.0 CD A:GLU177 2.9 14.9 1.0 CG A:ASP138 3.4 15.5 1.0 C A:GLU187 3.4 14.2 1.0 CG A:ASP185 3.4 17.9 1.0 OD2 A:ASP185 3.8 14.3 1.0 CA A:CA319 3.8 13.5 1.0 O A:HOH902 4.0 57.3 1.0 CB A:ASP138 4.0 9.3 1.0 N A:GLU187 4.2 15.2 1.0 CG A:GLU190 4.2 10.2 1.0 N A:ILE188 4.3 11.7 1.0 O A:ASP185 4.3 16.6 1.0 OD1 A:ASP138 4.3 15.3 1.0 CA A:ILE188 4.3 12.3 1.0 CA A:GLU187 4.4 12.7 1.0 CG A:GLU177 4.4 13.2 1.0 N A:GLY189 4.4 16.8 1.0 O A:HOH350 4.4 17.2 1.0 CB A:GLU187 4.6 12.5 1.0 C A:ASP185 4.7 19.4 1.0 C A:ILE188 4.8 20.6 1.0 CB A:ASP185 4.8 13.5 1.0 N A:ASP185 4.8 13.8 1.0 N A:GLU190 4.9 12.4 1.0 CB A:GLU177 4.9 10.3 1.0 O A:HOH353 4.9 16.7 1.0

Calcium binding site 2 out of 4 in the Thermolysin with Monocyclic 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 Monocyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:13.5 occ:1.00 OE2 A:GLU190 2.2 12.8 1.0 OE2 A:GLU177 2.2 15.2 1.0 OD2 A:ASP185 2.3 14.3 1.0 O A:HOH475 2.3 17.6 1.0 O A:ASN183 2.4 19.7 1.0 O A:HOH353 2.4 16.7 1.0 CD A:GLU177 3.2 14.9 1.0 CG A:ASP185 3.2 17.9 1.0 CD A:GLU190 3.3 10.6 1.0 C A:ASN183 3.6 12.8 1.0 OD1 A:ASP185 3.6 13.1 1.0 CG A:GLU190 3.7 10.2 1.0 CA A:CA318 3.8 12.7 1.0 OE1 A:GLU177 3.8 13.5 1.0 O A:LYS182 3.9 24.4 1.0 CB A:ASN183 4.1 18.9 1.0 O A:HOH905 4.1 80.5 1.0 CA A:PRO184 4.1 16.2 1.0 N A:ASP185 4.1 13.8 1.0 OD2 A:ASP191 4.2 16.0 1.0 C A:PRO184 4.2 31.9 1.0 CG A:GLU177 4.2 13.2 1.0 OE1 A:GLU190 4.3 12.5 1.0 N A:PRO184 4.3 21.6 1.0 OD1 A:ASP191 4.3 18.6 1.0 O A:HOH902 4.4 57.3 1.0 CB A:ASP185 4.4 13.5 1.0 CG A:ASP191 4.6 22.6 1.0 CA A:ASN183 4.6 14.8 1.0 CA A:ASP185 4.9 11.0 1.0 O A:PRO184 4.9 18.6 1.0 C A:LYS182 5.0 28.1 1.0

Calcium binding site 3 out of 4 in the Thermolysin with Monocyclic 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 Monocyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:13.8 occ:1.00 O A:GLN61 2.3 13.8 1.0 O A:HOH503 2.3 15.0 1.0 OD1 A:ASP59 2.4 15.4 1.0 O A:HOH482 2.4 19.5 1.0 OD1 A:ASP57 2.4 16.3 1.0 O A:HOH419 2.5 11.4 1.0 OD2 A:ASP57 2.6 15.9 1.0 CG A:ASP57 2.9 16.8 1.0 CG A:ASP59 3.3 26.6 1.0 C A:GLN61 3.5 19.6 1.0 OD2 A:ASP59 3.7 20.0 1.0 O A:HOH484 3.9 29.9 1.0 N A:GLN61 4.0 12.4 1.0 CA A:GLN61 4.2 11.1 1.0 N A:ASP59 4.3 13.7 1.0 CB A:GLN61 4.3 12.0 1.0 CB A:ASP57 4.4 7.7 1.0 O A:HOH628 4.4 45.9 1.0 O A:HOH508 4.5 18.1 1.0 N A:PHE62 4.5 14.8 1.0 OD2 A:ASP67 4.6 13.2 1.0 CA A:PHE62 4.6 10.9 1.0 O A:HOH356 4.6 13.3 1.0 CB A:ASP59 4.7 13.3 1.0 N A:ALA58 4.7 10.6 1.0 N A:ASN60 4.8 13.9 1.0 O A:HOH671 4.9 52.6 1.0 CA A:ASP59 4.9 11.5 1.0 C A:ASP59 4.9 14.2 1.0

Calcium binding site 4 out of 4 in the Thermolysin with Monocyclic 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 Monocyclic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca321 b:17.6 occ:1.00 OD1 A:ASP200 2.3 17.8 1.0 O A:ILE197 2.3 30.1 1.0 O A:HOH480 2.3 27.7 1.0 OG1 A:THR194 2.3 15.5 1.0 O A:THR194 2.3 16.8 1.0 O A:TYR193 2.4 14.0 1.0 O A:HOH354 2.5 16.1 1.0 C A:THR194 3.1 30.3 1.0 CG A:ASP200 3.3 16.3 1.0 CB A:THR194 3.4 14.9 1.0 C A:TYR193 3.4 16.3 1.0 C A:ILE197 3.5 36.8 1.0 CA A:THR194 3.7 14.8 1.0 OD2 A:ASP200 3.7 16.9 1.0 N A:THR194 4.0 19.2 1.0 N A:PRO195 4.1 20.5 1.0 N A:ILE197 4.2 33.6 1.0 CA A:ILE197 4.2 29.1 1.0 CB A:ILE197 4.2 27.2 1.0 O A:ASP200 4.4 18.5 1.0 N A:SER198 4.5 35.0 1.0 N A:ASP200 4.6 18.1 1.0 CA A:PRO195 4.6 25.3 1.0 O A:GLU190 4.6 14.3 1.0 CD2 A:TYR193 4.7 18.8 1.0 CA A:SER198 4.7 25.7 1.0 CA A:TYR193 4.7 12.8 1.0 CB A:ASP200 4.7 16.6 1.0 CG2 A:THR194 4.7 13.8 1.0 O A:HOH476 4.7 40.9 1.0 CB A:TYR193 4.7 17.5 1.0 C A:ASP200 4.8 9.4 1.0 C A:PRO195 4.8 33.8 1.0 CG2 A:ILE197 4.9 21.7 1.0 C A:SER198 5.0 29.6 1.0 CA A:ASP200 5.0 13.2 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.