Calcium in PDB 5n34: Thermolysin in Complex with Inhibitor JC276

All present enzymatic activity of Thermolysin in Complex with Inhibitor JC276:
3.4.24.27;

The structure of Thermolysin in Complex with Inhibitor JC276, PDB code: 5n34 was solved by J.Cramer, S.G.Krimmer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 1.22
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.529, 92.529, 129.916, 90.00, 90.00, 120.00
R / Rfree (%)	11 / 13

The structure of Thermolysin in Complex with Inhibitor JC276 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor JC276 (pdb code 5n34). 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 in Complex with Inhibitor JC276, PDB code: 5n34:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin in Complex with Inhibitor JC276


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with Inhibitor JC276 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:7.4 occ:1.00 O E:GLU187 2.3 8.4 1.0 OD2 E:ASP138 2.4 7.4 1.0 O E:HOH579 2.4 8.0 1.0 OE1 E:GLU177 2.5 7.6 1.0 OD1 E:ASP185 2.5 8.3 1.0 OE1 E:GLU190 2.5 7.8 1.0 OE2 E:GLU190 2.5 8.4 1.0 OE2 E:GLU177 2.8 8.0 1.0 CD E:GLU190 2.9 7.7 1.0 CD E:GLU177 2.9 7.3 1.0 CG E:ASP138 3.4 7.6 1.0 C E:GLU187 3.4 8.3 1.0 CG E:ASP185 3.5 8.4 1.0 HB3 E:ASP138 3.6 8.2 1.0 HA E:ILE188 3.6 8.8 1.0 H E:GLU187 3.7 10.9 1.0 H E:GLY189 3.8 8.9 1.0 CA E:CA404 3.8 9.1 1.0 OD2 E:ASP185 3.8 9.6 1.0 HB2 E:GLU187 3.9 14.1 1.0 CB E:ASP138 4.0 6.8 1.0 O E:ASP185 4.1 8.5 1.0 H E:GLU190 4.2 9.4 1.0 H E:ASP185 4.2 10.6 1.0 N E:GLU187 4.2 9.1 1.0 N E:ILE188 4.2 7.6 1.0 HB2 E:ASP138 4.2 8.2 1.0 OD1 E:ASP138 4.3 8.2 1.0 CA E:GLU187 4.3 9.0 1.0 CA E:ILE188 4.3 7.3 1.0 CG E:GLU190 4.3 8.3 1.0 HD13 E:ILE188 4.4 11.9 1.0 CG E:GLU177 4.4 7.2 1.0 N E:GLY189 4.4 7.5 1.0 O E:HOH577 4.4 11.6 1.0 C E:ASP185 4.6 8.1 1.0 HG3 E:GLU190 4.6 10.0 1.0 CB E:GLU187 4.6 11.7 1.0 HB2 E:GLU177 4.7 8.4 1.0 HB3 E:GLU177 4.7 8.4 1.0 CB E:ASP185 4.8 9.1 1.0 C E:ILE188 4.8 7.8 1.0 N E:ASP185 4.8 8.8 1.0 HG2 E:GLU190 4.8 10.0 1.0 HG2 E:GLU177 4.8 8.7 1.0 CB E:GLU177 4.9 7.0 1.0 HA E:THR174 4.9 7.4 1.0 HG3 E:GLU177 4.9 8.7 1.0 O E:HOH535 4.9 10.8 1.0 HB3 E:GLU190 5.0 10.4 1.0 N E:GLU190 5.0 7.8 1.0 CA E:ASP185 5.0 8.4 1.0

Calcium binding site 2 out of 4 in the Thermolysin in Complex with Inhibitor JC276


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with Inhibitor JC276 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca403 b:7.0 occ:1.00 O E:GLN61 2.3 6.7 1.0 O E:HOH760 2.3 10.1 1.0 OD1 E:ASP57 2.4 7.7 1.0 OD1 E:ASP59 2.4 7.4 1.0 O E:HOH574 2.4 9.1 1.0 O E:HOH601 2.4 8.5 1.0 OD2 E:ASP57 2.6 7.1 1.0 CG E:ASP57 2.8 6.8 1.0 H E:GLN61 3.3 8.5 1.0 CG E:ASP59 3.4 8.4 1.0 C E:GLN61 3.5 6.4 1.0 H E:ASP59 3.5 9.1 1.0 HB2 E:GLN61 3.7 11.9 1.0 OD2 E:ASP59 3.8 10.3 1.0 N E:GLN61 4.0 7.1 1.0 O E:HOH685 4.0 14.3 1.0 HA E:PHE62 4.0 7.6 1.0 CA E:GLN61 4.2 7.0 1.0 H E:ALA58 4.3 8.4 1.0 CB E:ASP57 4.3 7.0 1.0 N E:ASP59 4.3 7.6 1.0 H E:ASN60 4.4 8.1 1.0 CB E:GLN61 4.4 9.9 1.0 O E:HOH730 4.4 9.8 1.0 N E:PHE62 4.5 5.8 1.0 O E:HOH818 4.5 14.1 1.0 CB E:ASP59 4.6 7.9 1.0 N E:ASN60 4.6 6.8 1.0 O E:HOH525 4.6 7.3 1.0 OD2 E:ASP67 4.6 6.9 1.0 O E:HOH826 4.7 27.2 1.0 HB2 E:ASP57 4.7 8.4 1.0 N E:ALA58 4.7 7.0 1.0 O E:HOH815 4.7 24.7 1.0 CA E:PHE62 4.7 6.4 1.0 CA E:ASP59 4.8 7.8 1.0 HB3 E:ASP57 4.8 8.4 1.0 H E:PHE63 4.8 8.7 1.0 HB3 E:GLN61 4.9 11.9 1.0 HA E:ASP57 4.9 8.1 1.0 C E:ASP59 4.9 7.1 1.0 HB3 E:ASP59 4.9 9.5 1.0 HB3 E:ALA58 5.0 10.9 1.0

Calcium binding site 3 out of 4 in the Thermolysin in Complex with Inhibitor JC276


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with Inhibitor JC276 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca404 b:9.1 occ:1.00 O E:ASN183 2.3 10.6 1.0 OD2 E:ASP185 2.3 9.6 1.0 O E:HOH587 2.3 10.9 1.0 O E:HOH535 2.3 10.8 1.0 OE2 E:GLU190 2.3 8.4 1.0 OE2 E:GLU177 2.4 8.0 1.0 CD E:GLU177 3.2 7.3 1.0 CG E:ASP185 3.2 8.4 1.0 CD E:GLU190 3.3 7.7 1.0 C E:ASN183 3.5 11.1 1.0 HA E:PRO184 3.6 11.1 1.0 HG3 E:GLU190 3.6 10.0 1.0 OD1 E:ASP185 3.6 8.3 1.0 HB2 E:ASN183 3.7 18.4 1.0 OE1 E:GLU177 3.8 7.6 1.0 HB3 E:ASN183 3.8 18.4 1.0 HG2 E:GLU190 3.8 10.0 1.0 CA E:CA402 3.8 7.4 1.0 CG E:GLU190 3.8 8.3 1.0 H E:ASP185 4.0 10.6 1.0 CB E:ASN183 4.1 15.3 1.0 CA E:PRO184 4.1 9.3 1.0 N E:ASP185 4.2 8.8 1.0 OD2 E:ASP191 4.2 11.6 1.0 HG2 E:GLU177 4.2 8.7 1.0 CG E:GLU177 4.2 7.2 1.0 C E:PRO184 4.2 9.4 1.0 OD1 E:ASP191 4.3 10.9 1.0 N E:PRO184 4.3 9.7 1.0 OE1 E:GLU190 4.3 7.8 1.0 HG3 E:GLU177 4.3 8.7 1.0 HB3 E:ASP185 4.4 10.9 1.0 O E:LYS182 4.4 14.6 1.0 CB E:ASP185 4.4 9.1 1.0 CA E:ASN183 4.4 13.3 1.0 CG E:ASP191 4.5 10.0 1.0 O E:HOH808 4.5 29.8 1.0 CA E:ASP185 4.9 8.4 1.0 O E:PRO184 4.9 11.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin in Complex with Inhibitor JC276


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with Inhibitor JC276 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:11.3 occ:1.00 O E:ILE197 2.3 15.7 1.0 OD1 E:ASP200 2.4 11.2 1.0 O E:HOH738 2.4 18.4 1.0 O E:TYR193 2.4 10.7 1.0 O E:HOH603 2.4 12.8 1.0 OG1 E:THR194 2.4 12.3 1.0 O E:THR194 2.4 13.0 1.0 C E:THR194 3.2 12.3 1.0 C E:TYR193 3.4 10.4 1.0 CG E:ASP200 3.4 12.1 1.0 CB E:THR194 3.5 12.4 1.0 HB E:ILE197 3.5 22.2 1.0 C E:ILE197 3.5 16.2 1.0 H E:ILE197 3.6 19.9 1.0 CA E:THR194 3.6 11.8 1.0 HB E:THR194 3.7 14.9 1.0 OD2 E:ASP200 3.8 12.8 1.0 H E:ASP200 3.8 15.6 1.0 N E:THR194 3.9 10.9 1.0 HD2 E:TYR193 4.0 14.9 1.0 HB3 E:TYR193 4.0 13.0 1.0 HA E:SER198 4.0 21.8 1.0 HA E:PRO195 4.2 18.8 1.0 CA E:ILE197 4.2 16.8 1.0 CB E:ILE197 4.3 18.5 1.0 N E:PRO195 4.3 13.8 1.0 N E:ILE197 4.3 16.6 1.0 O E:HOH634 4.4 38.8 1.0 HG22 E:ILE197 4.4 22.3 1.0 O E:HOH616 4.5 34.1 1.0 O E:ASP200 4.5 12.3 1.0 N E:SER198 4.5 17.0 1.0 CA E:TYR193 4.5 9.9 1.0 HA E:THR194 4.6 14.1 1.0 H E:GLY199 4.6 19.2 1.0 O E:HOH767 4.6 27.6 1.0 CA E:SER198 4.6 18.1 1.0 N E:ASP200 4.6 13.0 1.0 CD2 E:TYR193 4.6 12.4 1.0 CB E:TYR193 4.7 10.8 1.0 CA E:PRO195 4.7 15.7 1.0 O E:GLU190 4.7 9.5 1.0 H E:THR194 4.7 13.1 1.0 CG2 E:THR194 4.7 12.8 1.0 CB E:ASP200 4.8 12.7 1.0 C E:ASP200 4.8 11.8 1.0 HG23 E:THR194 4.9 15.4 1.0 CG2 E:ILE197 4.9 18.6 1.0 H E:TYR193 4.9 10.9 1.0 C E:SER198 4.9 17.6 1.0 N E:GLY199 4.9 16.0 1.0 C E:PRO195 4.9 17.4 1.0 CA E:ASP200 5.0 12.5 1.0 HG21 E:THR194 5.0 15.4 1.0

J.Cramer, S.G.Krimmer, A.Heine, G.Klebe. Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in A Series of Thermolysin Inhibitors. J. Med. Chem. V. 60 5791 2017.
ISSN: ISSN 1520-4804
PubMed: 28590130
DOI: 10.1021/ACS.JMEDCHEM.7B00490