Calcium in PDB 4h57: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 4h57 was solved by L.Englert, A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.63 / 1.56
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.452, 92.452, 129.778, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 16.7

The structure of Thermolysin Inhibition also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin Inhibition (pdb code 4h57). 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 Inhibition, PDB code: 4h57:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin Inhibition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.2 occ:1.00 OD2 A:ASP138 2.4 9.8 1.0 O A:GLU187 2.4 11.3 1.0 OD1 A:ASP185 2.4 11.7 1.0 OE1 A:GLU177 2.4 10.5 1.0 O A:HOH641 2.5 13.6 1.0 OE2 A:GLU190 2.5 13.0 1.0 OE1 A:GLU190 2.5 12.1 1.0 OE2 A:GLU177 2.7 13.4 1.0 CD A:GLU190 2.8 13.6 1.0 CD A:GLU177 2.9 13.8 1.0 CG A:ASP138 3.3 11.5 1.0 C A:GLU187 3.4 10.5 1.0 CG A:ASP185 3.5 12.4 1.0 CA A:CA402 3.8 12.7 1.0 OD2 A:ASP185 3.9 12.5 1.0 CB A:ASP138 4.0 8.8 1.0 O A:ASP185 4.1 11.9 1.0 N A:GLU187 4.2 12.4 1.0 OD1 A:ASP138 4.2 12.4 1.0 N A:ILE188 4.3 10.2 1.0 CA A:GLU187 4.3 11.1 1.0 CA A:ILE188 4.3 11.2 1.0 CG A:GLU190 4.3 13.9 1.0 CG A:GLU177 4.4 11.0 1.0 O A:HOH527 4.4 15.5 1.0 N A:GLY189 4.4 11.3 1.0 CB A:GLU187 4.5 11.1 1.0 C A:ASP185 4.6 10.9 1.0 N A:ASP185 4.7 12.2 1.0 CB A:ASP185 4.8 12.9 1.0 C A:ILE188 4.8 11.7 1.0 CB A:GLU177 4.9 11.5 1.0 O A:HOH642 4.9 16.6 1.0 N A:GLU190 5.0 13.1 1.0 CA A:ASP185 5.0 12.0 1.0

Calcium binding site 2 out of 4 in the Thermolysin Inhibition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:12.7 occ:1.00 O A:ASN183 2.3 14.5 1.0 O A:HOH642 2.3 16.6 1.0 OE2 A:GLU190 2.3 13.0 1.0 OE2 A:GLU177 2.3 13.4 1.0 OD2 A:ASP185 2.4 12.5 1.0 O A:HOH624 2.4 16.1 1.0 CG A:ASP185 3.2 12.4 1.0 CD A:GLU177 3.2 13.8 1.0 CD A:GLU190 3.3 13.6 1.0 C A:ASN183 3.4 15.2 1.0 OD1 A:ASP185 3.6 11.7 1.0 OE1 A:GLU177 3.8 10.5 1.0 CA A:CA401 3.8 11.2 1.0 CG A:GLU190 3.8 13.9 1.0 CA A:PRO184 4.1 14.6 1.0 CB A:ASN183 4.1 17.3 1.0 N A:ASP185 4.2 12.2 1.0 OD2 A:ASP191 4.2 17.9 1.0 C A:PRO184 4.2 15.1 1.0 CG A:GLU177 4.2 11.0 1.0 OD1 A:ASP191 4.2 18.4 1.0 N A:PRO184 4.3 13.3 1.0 OE1 A:GLU190 4.3 12.1 1.0 O A:LYS182 4.4 17.1 1.0 CB A:ASP185 4.4 12.9 1.0 CA A:ASN183 4.5 17.6 1.0 CG A:ASP191 4.5 17.8 1.0 O A:PRO184 4.9 15.0 1.0 CA A:ASP185 4.9 12.0 1.0

Calcium binding site 3 out of 4 in the Thermolysin Inhibition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:12.1 occ:1.00 O A:GLN61 2.3 11.5 1.0 OD2 A:ASP57 2.4 11.7 1.0 O A:HOH640 2.4 16.0 1.0 O A:HOH634 2.4 14.9 1.0 OD1 A:ASP59 2.4 11.8 1.0 O A:HOH631 2.4 13.0 1.0 OD1 A:ASP57 2.5 10.6 1.0 CG A:ASP57 2.8 11.1 1.0 CG A:ASP59 3.4 13.2 1.0 C A:GLN61 3.5 10.6 1.0 OD2 A:ASP59 3.8 15.8 1.0 N A:GLN61 4.0 11.9 1.0 O A:HOH561 4.0 17.6 1.0 CA A:GLN61 4.1 11.5 0.3 CA A:GLN61 4.1 10.9 0.7 CB A:GLN61 4.3 12.3 0.3 CB A:ASP57 4.3 10.0 1.0 N A:ASP59 4.3 11.1 1.0 CB A:GLN61 4.4 12.8 0.7 O A:HOH573 4.5 25.6 1.0 N A:PHE62 4.5 10.8 1.0 OD2 A:ASP67 4.6 11.1 1.0 O A:HOH505 4.6 11.7 1.0 CB A:ASP59 4.6 11.6 1.0 N A:ASN60 4.7 12.3 1.0 O A:HOH687 4.7 40.8 1.0 O A:HOH639 4.7 34.1 1.0 N A:ALA58 4.7 11.4 1.0 CA A:ASP59 4.8 11.1 1.0 CA A:PHE62 4.8 10.2 1.0 C A:ASP59 4.9 11.4 1.0

Calcium binding site 4 out of 4 in the Thermolysin Inhibition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:14.7 occ:1.00 O A:ILE197 2.3 15.0 1.0 O A:TYR193 2.3 13.7 1.0 O A:HOH574 2.3 18.2 1.0 O A:THR194 2.4 16.6 1.0 OG1 A:THR194 2.4 16.7 1.0 OD1 A:ASP200 2.4 15.5 1.0 O A:HOH799 2.4 24.5 1.0 C A:THR194 3.2 15.6 1.0 C A:TYR193 3.4 14.3 1.0 CB A:THR194 3.4 16.9 1.0 C A:ILE197 3.4 18.0 1.0 CG A:ASP200 3.5 18.6 1.0 CA A:THR194 3.7 14.3 1.0 OD2 A:ASP200 3.9 19.1 1.0 N A:THR194 3.9 13.9 1.0 CA A:ILE197 4.2 21.1 1.0 CB A:ILE197 4.2 20.6 1.0 N A:PRO195 4.3 14.8 1.0 N A:ILE197 4.3 23.3 1.0 O A:HOH638 4.4 34.9 1.0 O A:ASP200 4.4 16.7 1.0 N A:SER198 4.5 20.9 1.0 CA A:TYR193 4.6 12.7 1.0 O A:GLU190 4.6 13.4 1.0 N A:ASP200 4.6 16.6 1.0 CA A:SER198 4.7 20.3 0.6 CA A:PRO195 4.7 17.0 1.0 O A:HOH814 4.7 31.4 1.0 CA A:SER198 4.7 20.7 0.4 CD2 A:TYR193 4.7 15.4 1.0 CB A:TYR193 4.7 13.8 1.0 CG2 A:THR194 4.7 18.9 1.0 CB A:ASP200 4.8 17.1 1.0 C A:ASP200 4.8 15.2 1.0 CG2 A:ILE197 4.8 19.9 1.0 CA A:ASP200 5.0 14.8 1.0 C A:SER198 5.0 19.2 1.0 N A:GLY199 5.0 18.9 1.0 C A:PRO195 5.0 20.7 1.0

A.Biela, N.N.Nasief, M.Betz, A.Heine, D.Hangauer, G.Klebe. Dissecting the Hydrophobic Effect on the Molecular Level: the Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin. Angew.Chem.Int.Ed.Engl. V. 52 1822 2013.
ISSN: ISSN 1433-7851
PubMed: 23283700
DOI: 10.1002/ANIE.201208561