Calcium in PDB 2whz: Dipeptide Inhibitors of Thermolysin

All present enzymatic activity of Dipeptide Inhibitors of Thermolysin:
3.4.24.27;

The structure of Dipeptide Inhibitors of Thermolysin, PDB code: 2whz was solved by B.A.Lund, I.Leiros, H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.890, 92.890, 127.740, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 19.7

The structure of Dipeptide Inhibitors of Thermolysin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Dipeptide Inhibitors of Thermolysin (pdb code 2whz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Dipeptide Inhibitors of Thermolysin, PDB code: 2whz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Dipeptide Inhibitors of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dipeptide Inhibitors of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1318 b:12.4 occ:1.00 O A:GLU187 2.3 12.8 1.0 OD2 A:ASP138 2.4 13.9 1.0 O A:HOH2232 2.4 13.3 1.0 OD1 A:ASP185 2.5 13.1 1.0 OE2 A:GLU190 2.5 11.9 1.0 OE1 A:GLU190 2.5 14.6 1.0 OE1 A:GLU177 2.5 12.3 1.0 CD A:GLU190 2.8 13.2 1.0 OE2 A:GLU177 2.9 12.8 1.0 CD A:GLU177 3.0 13.5 1.0 CG A:ASP138 3.4 13.8 1.0 C A:GLU187 3.4 13.5 1.0 CG A:ASP185 3.5 16.8 1.0 CA A:CA1319 3.8 15.1 1.0 OD2 A:ASP185 3.9 14.7 1.0 CB A:ASP138 4.0 12.0 1.0 O A:ASP185 4.2 14.7 1.0 N A:GLU187 4.2 14.6 1.0 N A:ILE188 4.2 14.3 1.0 O A:HOH2204 4.2 33.4 1.0 OD1 A:ASP138 4.3 12.4 1.0 CA A:ILE188 4.3 13.5 1.0 CA A:GLU187 4.3 15.0 1.0 CG A:GLU190 4.3 13.6 1.0 N A:GLY189 4.4 13.7 1.0 CG A:GLU177 4.5 13.5 1.0 O A:HOH2205 4.5 14.7 1.0 CB A:GLU187 4.6 14.9 1.0 C A:ASP185 4.6 15.4 1.0 CB A:ASP185 4.8 15.7 1.0 C A:ILE188 4.8 14.6 1.0 N A:ASP185 4.9 15.7 1.0 CB A:GLU177 4.9 11.8 1.0 N A:GLU190 4.9 14.6 1.0

Calcium binding site 2 out of 4 in the Dipeptide Inhibitors of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dipeptide Inhibitors of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1319 b:15.1 occ:1.00 O A:ASN183 2.3 18.3 1.0 OE2 A:GLU190 2.3 11.9 1.0 O A:HOH2241 2.3 15.1 1.0 OE2 A:GLU177 2.3 12.8 1.0 OD2 A:ASP185 2.4 14.7 1.0 O A:HOH2240 2.4 15.2 1.0 CD A:GLU177 3.2 13.5 1.0 CG A:ASP185 3.3 16.8 1.0 CD A:GLU190 3.3 13.2 1.0 C A:ASN183 3.5 17.8 1.0 OD1 A:ASP185 3.7 13.1 1.0 OE1 A:GLU177 3.7 12.3 1.0 CG A:GLU190 3.8 13.6 1.0 CA A:CA1318 3.8 12.4 1.0 CA A:PRO184 4.1 17.2 1.0 CB A:ASN183 4.1 18.3 1.0 OD2 A:ASP191 4.2 17.4 1.0 C A:PRO184 4.2 17.1 1.0 CG A:GLU177 4.2 13.5 1.0 N A:ASP185 4.2 15.7 1.0 OD1 A:ASP191 4.3 15.2 1.0 N A:PRO184 4.3 17.9 1.0 O A:LYS182 4.3 21.9 1.0 OE1 A:GLU190 4.3 14.6 1.0 CB A:ASP185 4.4 15.7 1.0 CA A:ASN183 4.5 18.9 1.0 O A:HOH2115 4.5 39.1 1.0 O A:HOH2204 4.5 33.4 1.0 O A:HOH2233 4.5 40.3 1.0 CG A:ASP191 4.6 16.4 1.0 O A:PRO184 4.8 16.4 1.0 CA A:ASP185 5.0 15.9 1.0

Calcium binding site 3 out of 4 in the Dipeptide Inhibitors of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dipeptide Inhibitors of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1320 b:12.7 occ:1.00 O A:HOH2109 2.3 14.3 1.0 O A:GLN61 2.4 11.6 1.0 OD1 A:ASP57 2.4 12.2 1.0 OD1 A:ASP59 2.4 12.2 1.0 O A:HOH2112 2.5 12.2 1.0 O A:HOH2128 2.5 11.4 1.0 OD2 A:ASP57 2.5 8.8 1.0 CG A:ASP57 2.8 10.8 1.0 CG A:ASP59 3.4 15.3 1.0 C A:GLN61 3.5 11.2 1.0 OD2 A:ASP59 3.8 14.6 1.0 N A:GLN61 4.0 12.3 1.0 O A:HOH2119 4.0 17.6 1.0 CA A:GLN61 4.2 11.7 1.0 CB A:ASP57 4.3 11.6 1.0 N A:ASP59 4.3 13.0 1.0 CB A:GLN61 4.4 12.4 1.0 O A:HOH2110 4.4 13.4 1.0 O A:HOH2108 4.5 11.5 1.0 N A:PHE62 4.6 10.5 1.0 OD2 A:ASP67 4.6 12.1 1.0 CB A:ASP59 4.6 13.9 1.0 O A:HOH2050 4.6 34.5 1.0 O A:HOH2056 4.7 30.1 1.0 N A:ASN60 4.7 12.8 1.0 N A:ALA58 4.7 12.2 1.0 CA A:ASP59 4.8 13.2 1.0 CA A:PHE62 4.8 11.0 1.0 C A:ASP59 4.9 12.7 1.0 CA A:ASP57 5.0 11.7 1.0

Calcium binding site 4 out of 4 in the Dipeptide Inhibitors of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dipeptide Inhibitors of Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1321 b:16.6 occ:1.00 O A:TYR193 2.3 13.3 1.0 O A:ILE197 2.3 22.5 1.0 O A:HOH2243 2.3 25.1 1.0 O A:THR194 2.4 18.3 1.0 OD1 A:ASP200 2.4 19.3 1.0 OG1 A:THR194 2.4 16.3 1.0 O A:HOH2236 2.4 20.1 1.0 C A:THR194 3.2 17.0 1.0 C A:TYR193 3.3 14.1 1.0 CB A:THR194 3.4 15.1 1.0 CG A:ASP200 3.5 17.3 1.0 C A:ILE197 3.5 24.8 1.0 CA A:THR194 3.6 16.0 1.0 OD2 A:ASP200 3.8 17.1 1.0 N A:THR194 3.8 14.4 1.0 O A:HOH2237 3.9 32.3 1.0 CA A:ILE197 4.2 25.0 1.0 CB A:ILE197 4.2 24.7 1.0 N A:ILE197 4.2 24.9 1.0 N A:PRO195 4.4 17.8 1.0 CA A:TYR193 4.5 14.1 1.0 N A:SER198 4.5 24.2 1.0 O A:ASP200 4.6 16.6 1.0 O A:GLU190 4.6 15.0 1.0 O A:HOH2238 4.6 30.2 1.0 N A:ASP200 4.7 19.9 1.0 CB A:TYR193 4.7 15.0 1.0 CG2 A:THR194 4.7 17.3 1.0 CD2 A:TYR193 4.7 19.6 1.0 CB A:ASP200 4.8 18.9 1.0 CA A:SER198 4.8 25.4 1.0 CA A:PRO195 4.8 19.5 1.0 CG2 A:ILE197 4.9 25.1 1.0 C A:ASP200 4.9 17.7 1.0 C A:SER198 5.0 24.5 1.0 CA A:ASP200 5.0 18.7 1.0

B.A.Lund, I.Leiros, H.-K.S.Leiros. Dipeptide Inhibitors of Thermolysin To Be Published.