Calcium in PDB 5m69: Thermolysin in Complex with Inhibitor and Xenon

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

The structure of Thermolysin in Complex with Inhibitor and Xenon, PDB code: 5m69 was solved by S.G.Krimmer, J.Cramer, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.24 / 1.44
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.476, 92.476, 129.938, 90.00, 90.00, 120.00
R / Rfree (%)	10.8 / 14.1

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

Xenon	(Xe)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Thermolysin in Complex with Inhibitor and Xenon (pdb code 5m69). 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 and Xenon, PDB code: 5m69:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 and Xenon within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:11.4 occ:1.00 O E:GLN61 2.3 11.0 1.0 O E:HOH745 2.3 14.6 1.0 OD1 E:ASP57 2.3 11.4 1.0 OD1 E:ASP59 2.4 12.4 1.0 O E:HOH587 2.4 13.1 1.0 O E:HOH534 2.4 14.5 1.0 OD2 E:ASP57 2.6 11.5 1.0 CG E:ASP57 2.8 10.8 1.0 H E:GLN61 3.3 12.8 1.0 CG E:ASP59 3.4 12.5 1.0 C E:GLN61 3.4 10.0 1.0 H E:ASP59 3.6 12.9 1.0 OD2 E:ASP59 3.8 16.0 1.0 O E:HOH676 3.9 18.5 1.0 N E:GLN61 4.0 10.7 1.0 HA E:PHE62 4.0 12.2 1.0 CA E:GLN61 4.2 10.4 1.0 CB E:ASP57 4.3 11.5 1.0 CB E:GLN61 4.3 12.9 1.0 N E:ASP59 4.3 10.8 1.0 H E:ALA58 4.4 13.1 1.0 H E:ASN60 4.4 12.5 1.0 N E:PHE62 4.5 9.6 1.0 O E:HOH520 4.6 11.4 1.0 CB E:ASP59 4.6 11.7 1.0 OD2 E:ASP67 4.6 10.7 1.0 O E:HOH820 4.7 31.9 1.0 HB2 E:ASP57 4.7 13.8 1.0 N E:ASN60 4.7 10.4 1.0 CA E:PHE62 4.7 10.1 1.0 HB3 E:ASP57 4.8 13.8 1.0 N E:ALA58 4.8 10.9 1.0 H E:PHE63 4.8 13.2 1.0 CA E:ASP59 4.8 11.0 1.0 HA E:ASP57 4.8 13.5 1.0 C E:ASP59 4.9 11.2 1.0 HB3 E:ASP59 5.0 14.0 1.0

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


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 and Xenon within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca403 b:10.8 occ:1.00 O E:GLU187 2.3 12.0 1.0 OD2 E:ASP138 2.4 11.1 1.0 O E:HOH547 2.4 11.3 1.0 OD1 E:ASP185 2.5 11.7 1.0 OE1 E:GLU190 2.5 12.1 1.0 OE1 E:GLU177 2.5 11.6 1.0 OE2 E:GLU190 2.5 12.4 1.0 OE2 E:GLU177 2.7 12.4 1.0 CD E:GLU190 2.8 11.8 1.0 CD E:GLU177 2.9 11.2 1.0 CG E:ASP138 3.4 11.7 1.0 C E:GLU187 3.4 11.6 1.0 CG E:ASP185 3.5 12.6 1.0 HB3 E:ASP138 3.6 11.3 1.0 HA E:ILE188 3.6 14.1 1.0 H E:GLU187 3.7 14.8 1.0 H E:GLY189 3.8 13.5 1.0 CA E:CA404 3.8 13.3 1.0 OD2 E:ASP185 3.8 14.1 1.0 HB2 E:GLU187 3.9 17.7 1.0 CB E:ASP138 4.0 9.4 1.0 O E:ASP185 4.1 11.6 1.0 H E:GLU190 4.2 14.7 1.0 H E:ASP185 4.2 14.8 1.0 N E:GLU187 4.2 12.3 1.0 N E:ILE188 4.2 11.5 1.0 OD1 E:ASP138 4.3 13.2 1.0 CA E:GLU187 4.3 12.9 1.0 HB2 E:ASP138 4.3 11.3 1.0 CG E:GLU190 4.3 12.5 1.0 CA E:ILE188 4.3 11.7 1.0 HD13 E:ILE188 4.3 17.4 1.0 CG E:GLU177 4.4 11.4 1.0 O E:HOH536 4.4 17.1 1.0 N E:GLY189 4.4 11.2 1.0 CB E:GLU187 4.6 14.8 1.0 HG3 E:GLU190 4.6 15.1 1.0 C E:ASP185 4.6 11.9 1.0 HB2 E:GLU177 4.7 13.8 1.0 CB E:ASP185 4.8 12.2 1.0 N E:ASP185 4.8 12.4 1.0 HB3 E:GLU177 4.8 13.8 1.0 HG2 E:GLU190 4.8 15.1 1.0 C E:ILE188 4.8 11.1 1.0 HG2 E:GLU177 4.8 13.7 1.0 O E:HOH585 4.9 16.6 1.0 CB E:GLU177 4.9 11.5 1.0 HA E:THR174 4.9 10.9 1.0 HG3 E:GLU177 4.9 13.7 1.0 HB3 E:GLU190 4.9 14.9 1.0 N E:GLU190 5.0 12.3 1.0 CA E:ASP185 5.0 11.9 1.0

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


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 and Xenon within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca404 b:13.3 occ:1.00 O E:ASN183 2.3 14.9 1.0 OE2 E:GLU190 2.3 12.4 1.0 O E:HOH585 2.3 16.6 1.0 OD2 E:ASP185 2.3 14.1 1.0 O E:HOH565 2.4 16.9 1.0 OE2 E:GLU177 2.4 12.4 1.0 CG E:ASP185 3.2 12.6 1.0 CD E:GLU177 3.2 11.2 1.0 CD E:GLU190 3.4 11.8 1.0 C E:ASN183 3.5 14.9 1.0 HA E:PRO184 3.5 15.8 1.0 HG3 E:GLU190 3.6 15.1 1.0 OD1 E:ASP185 3.6 11.7 1.0 HB2 E:ASN183 3.8 23.8 1.0 OE1 E:GLU177 3.8 11.6 1.0 HB3 E:ASN183 3.8 23.8 1.0 HG2 E:GLU190 3.8 15.1 1.0 CA E:CA403 3.8 10.8 1.0 CG E:GLU190 3.9 12.5 1.0 H E:ASP185 4.0 14.8 1.0 CA E:PRO184 4.1 13.2 1.0 CB E:ASN183 4.1 19.8 1.0 N E:ASP185 4.2 12.4 1.0 OD2 E:ASP191 4.2 17.4 1.0 HG2 E:GLU177 4.2 13.7 1.0 OD1 E:ASP191 4.2 17.4 1.0 C E:PRO184 4.2 13.2 1.0 CG E:GLU177 4.2 11.4 1.0 N E:PRO184 4.3 13.2 1.0 OE1 E:GLU190 4.3 12.1 1.0 HG3 E:GLU177 4.3 13.7 1.0 HB3 E:ASP185 4.4 14.6 1.0 CB E:ASP185 4.4 12.2 1.0 O E:HOH743 4.4 40.7 1.0 O E:LYS182 4.4 17.7 1.0 CA E:ASN183 4.5 17.0 1.0 CG E:ASP191 4.6 16.6 1.0 CA E:ASP185 4.9 11.9 1.0 O E:PRO184 4.9 14.7 1.0 O E:HOH736 5.0 39.5 1.0

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


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 and Xenon within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:14.5 occ:1.00 O E:ILE197 2.3 19.1 1.0 O E:TYR193 2.3 14.1 1.0 OD1 E:ASP200 2.4 15.2 1.0 O E:HOH720 2.4 23.3 1.0 O E:HOH597 2.4 15.9 1.0 O E:THR194 2.4 16.2 1.0 OG1 E:THR194 2.4 15.2 1.0 C E:THR194 3.2 15.3 1.0 C E:TYR193 3.4 13.8 1.0 CG E:ASP200 3.4 15.0 1.0 HB E:ILE197 3.4 26.6 1.0 CB E:THR194 3.5 16.0 1.0 C E:ILE197 3.5 19.8 1.0 H E:ILE197 3.6 27.2 1.0 CA E:THR194 3.7 14.9 1.0 HB E:THR194 3.7 19.2 1.0 OD2 E:ASP200 3.8 17.1 1.0 H E:ASP200 3.9 20.2 1.0 N E:THR194 3.9 14.3 1.0 HA E:SER198 4.0 27.4 1.0 HB3 E:TYR193 4.1 17.3 1.0 HD2 E:TYR193 4.1 20.3 1.0 CB E:ILE197 4.2 22.2 1.0 CA E:ILE197 4.2 21.4 1.0 N E:ILE197 4.3 22.7 1.0 N E:PRO195 4.3 17.1 1.0 HA E:PRO195 4.3 23.2 1.0 HG22 E:ILE197 4.4 27.7 1.0 O E:ASP200 4.5 15.5 1.0 N E:SER198 4.5 21.1 1.0 O E:HOH658 4.5 35.0 1.0 CA E:TYR193 4.6 13.3 1.0 O E:HOH754 4.6 30.6 1.0 HA E:THR194 4.6 17.9 1.0 N E:ASP200 4.6 16.9 1.0 CA E:SER198 4.6 22.9 1.0 O E:GLU190 4.7 13.6 1.0 CB E:TYR193 4.7 14.4 1.0 CD2 E:TYR193 4.7 16.9 1.0 CA E:PRO195 4.7 19.3 1.0 CB E:ASP200 4.7 15.1 1.0 H E:THR194 4.8 17.2 1.0 CG2 E:THR194 4.8 16.9 1.0 C E:ASP200 4.8 14.7 1.0 CG2 E:ILE197 4.9 23.1 1.0 HG23 E:THR194 4.9 20.3 1.0 C E:SER198 4.9 22.0 1.0 N E:GLY199 4.9 20.1 1.0 CA E:ASP200 4.9 15.2 1.0 H E:TYR193 5.0 14.6 1.0 C E:PRO195 5.0 22.1 1.0

S.G.Krimmer, J.Cramer, J.Schiebel, A.Heine, G.Klebe. How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin. J. Am. Chem. Soc. V. 139 10419 2017.
ISSN: ESSN 1520-5126
PubMed: 28696673
DOI: 10.1021/JACS.7B05028