Calcium in PDB 3f28: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3f28 was solved by L.Englert, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.68
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.520, 92.520, 128.946, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23.6

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 3f28). 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: 3f28:
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:Ca317 b:18.3 occ:1.00 O A:GLU187 2.3 19.4 1.0 OD2 A:ASP138 2.3 20.3 1.0 O A:HOH1504 2.4 20.4 1.0 OE2 A:GLU190 2.5 18.5 1.0 OE1 A:GLU177 2.5 18.5 1.0 OD1 A:ASP185 2.5 21.4 1.0 OE1 A:GLU190 2.5 17.8 1.0 OE2 A:GLU177 2.8 19.7 1.0 CD A:GLU190 2.8 18.6 1.0 CD A:GLU177 2.9 24.9 1.0 C A:GLU187 3.3 16.1 1.0 CG A:ASP138 3.4 25.7 1.0 CG A:ASP185 3.5 22.4 1.0 OD2 A:ASP185 3.8 19.1 1.0 CA A:CA318 3.8 20.9 1.0 CB A:ASP138 4.0 14.1 1.0 O A:ASP185 4.1 19.2 1.0 N A:GLU187 4.2 19.0 1.0 N A:ILE188 4.2 19.6 1.0 CA A:GLU187 4.3 19.2 1.0 OD1 A:ASP138 4.3 23.1 1.0 CA A:ILE188 4.3 18.4 1.0 CG A:GLU190 4.3 20.1 1.0 CG A:GLU177 4.4 17.3 1.0 N A:GLY189 4.4 17.8 1.0 O A:HOH1503 4.4 25.9 1.0 C A:ASP185 4.6 25.1 1.0 CB A:GLU187 4.6 22.4 1.0 CB A:ASP185 4.7 16.4 1.0 C A:ILE188 4.8 20.6 1.0 N A:ASP185 4.8 19.9 1.0 CB A:GLU177 4.9 13.7 1.0 N A:GLU190 5.0 24.5 1.0 CA A:ASP185 5.0 17.6 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:Ca318 b:20.9 occ:1.00 OD2 A:ASP185 2.3 19.1 1.0 O A:HOH1432 2.3 23.3 1.0 O A:ASN183 2.3 21.6 1.0 OE2 A:GLU190 2.3 18.5 1.0 O A:HOH1505 2.3 25.7 1.0 OE2 A:GLU177 2.4 19.7 1.0 CG A:ASP185 3.2 22.4 1.0 CD A:GLU177 3.3 24.9 1.0 CD A:GLU190 3.3 18.6 1.0 C A:ASN183 3.5 20.3 1.0 OD1 A:ASP185 3.6 21.4 1.0 OE1 A:GLU177 3.8 18.5 1.0 CG A:GLU190 3.8 20.1 1.0 CA A:CA317 3.8 18.3 1.0 CA A:PRO184 4.1 19.2 1.0 OD1 A:ASP191 4.2 30.2 1.0 CB A:ASN183 4.2 23.6 1.0 N A:ASP185 4.2 19.9 1.0 C A:PRO184 4.2 26.3 1.0 OD2 A:ASP191 4.3 29.8 1.0 CG A:GLU177 4.3 17.3 1.0 N A:PRO184 4.3 19.6 1.0 OE1 A:GLU190 4.3 17.8 1.0 O A:LYS182 4.4 25.9 1.0 CB A:ASP185 4.4 16.4 1.0 CA A:ASN183 4.5 22.6 1.0 CG A:ASP191 4.5 33.7 1.0 O A:HOH1444 4.5 38.5 1.0 O A:PRO184 4.9 23.5 1.0 CA A:ASP185 4.9 17.6 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:Ca319 b:19.8 occ:1.00 O A:HOH1487 2.3 25.4 1.0 OD2 A:ASP57 2.3 18.9 1.0 O A:GLN61 2.3 17.6 1.0 O A:HOH1508 2.4 19.5 1.0 OD1 A:ASP59 2.4 21.1 1.0 O A:HOH1507 2.5 23.8 1.0 OD1 A:ASP57 2.6 21.0 1.0 CG A:ASP57 2.8 22.9 1.0 CG A:ASP59 3.4 27.1 1.0 C A:GLN61 3.5 16.0 1.0 OD2 A:ASP59 3.6 25.4 1.0 O A:HOH1415 3.9 25.8 1.0 N A:GLN61 4.0 20.9 1.0 CA A:GLN61 4.1 18.4 1.0 O A:HOH1523 4.2 41.0 1.0 CB A:ASP57 4.3 17.8 1.0 O A:HOH1433 4.3 24.6 1.0 CB A:GLN61 4.3 21.8 1.0 N A:ASP59 4.4 20.6 1.0 N A:PHE62 4.6 16.2 1.0 OD2 A:ASP67 4.6 21.2 1.0 O A:HOH1425 4.6 19.8 1.0 CB A:ASP59 4.6 22.7 1.0 N A:ASN60 4.7 16.4 1.0 N A:ALA58 4.7 20.4 1.0 CA A:PHE62 4.8 17.4 1.0 CA A:ASP59 4.9 23.8 1.0 C A:ASP59 4.9 22.9 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:Ca320 b:23.1 occ:1.00 O A:THR194 2.2 30.6 1.0 O A:ILE197 2.3 29.7 1.0 O A:HOH1510 2.3 31.8 1.0 OG1 A:THR194 2.4 24.1 1.0 O A:TYR193 2.4 21.2 1.0 OD1 A:ASP200 2.4 20.6 1.0 O A:HOH1468 2.6 24.5 1.0 C A:THR194 3.1 31.0 1.0 C A:TYR193 3.3 25.4 1.0 C A:ILE197 3.4 34.5 1.0 CB A:THR194 3.4 24.3 1.0 CG A:ASP200 3.5 20.5 1.0 CA A:THR194 3.6 29.9 1.0 N A:THR194 3.8 24.0 1.0 OD2 A:ASP200 4.0 24.9 1.0 CA A:ILE197 4.1 36.6 1.0 CB A:ILE197 4.1 38.8 1.0 N A:PRO195 4.2 22.8 1.0 N A:ILE197 4.3 32.8 1.0 N A:SER198 4.5 28.4 1.0 CA A:SER198 4.5 20.9 1.0 CA A:TYR193 4.5 17.9 1.0 N A:ASP200 4.6 23.6 1.0 O A:ASP200 4.6 23.6 1.0 CA A:PRO195 4.6 21.7 1.0 CD2 A:TYR193 4.7 23.8 1.0 CB A:TYR193 4.7 17.0 1.0 O A:GLU190 4.7 22.4 1.0 CG2 A:THR194 4.7 26.1 1.0 CB A:ASP200 4.8 20.7 1.0 C A:SER198 4.8 26.4 1.0 CG2 A:ILE197 4.8 36.1 1.0 C A:ASP200 4.9 18.4 1.0 N A:GLY199 4.9 33.7 1.0 C A:PRO195 5.0 27.2 1.0

L.Englert, K.Silber, H.Steuber, S.Brass, B.Over, H.D.Gerber, A.Heine, W.E.Diederich, G.Klebe. Fragment-Based Lead Discovery: Screening and Optimizing Fragments For Thermolysin Inhibition. Chemmedchem V. 5 930 2010.
ISSN: ISSN 1860-7179
PubMed: 20394106
DOI: 10.1002/CMDC.201000084