Calcium in PDB 3fcq: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3fcq was solved by H.Steuber, L.Englert, K.Silber, 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 / 1.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.718, 92.718, 129.965, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 23.1

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 3fcq). 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: 3fcq:
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:Ca323 b:10.9 occ:1.00 O A:GLU187 2.3 11.8 1.0 OD2 A:ASP138 2.3 10.6 1.0 OE1 A:GLU177 2.5 10.8 1.0 OE1 A:GLU190 2.5 11.4 1.0 OE2 A:GLU190 2.5 11.7 1.0 OD1 A:ASP185 2.5 12.8 1.0 O A:HOH2238 2.5 8.8 1.0 OE2 A:GLU177 2.8 10.1 1.0 CD A:GLU190 2.8 11.2 1.0 CD A:GLU177 2.9 13.6 1.0 C A:GLU187 3.3 7.4 1.0 CG A:ASP138 3.4 9.7 1.0 CG A:ASP185 3.5 16.4 1.0 CA A:CA324 3.8 14.0 1.0 OD2 A:ASP185 3.9 12.9 1.0 CB A:ASP138 4.0 8.7 1.0 N A:GLU187 4.2 13.1 1.0 N A:ILE188 4.2 10.5 1.0 O A:ASP185 4.2 14.8 1.0 CA A:GLU187 4.2 13.1 1.0 CA A:ILE188 4.2 10.4 1.0 OD1 A:ASP138 4.2 11.4 1.0 O A:HOH2066 4.3 15.4 1.0 CG A:GLU190 4.3 9.9 1.0 N A:GLY189 4.3 10.4 1.0 CG A:GLU177 4.4 8.9 1.0 CB A:GLU187 4.6 10.6 1.0 C A:ASP185 4.6 18.0 1.0 C A:ILE188 4.7 10.8 1.0 N A:ASP185 4.7 11.6 1.0 CB A:ASP185 4.8 12.2 1.0 N A:GLU190 4.9 10.0 1.0 CB A:GLU177 4.9 7.8 1.0 O A:HOH2208 4.9 15.1 1.0 CA A:ASP185 5.0 9.7 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:Ca324 b:14.0 occ:1.00 O A:HOH2198 2.3 13.9 1.0 O A:HOH2208 2.3 15.1 1.0 OE2 A:GLU190 2.3 11.7 1.0 OD2 A:ASP185 2.4 12.9 1.0 O A:ASN183 2.5 16.1 1.0 OE2 A:GLU177 2.5 10.1 1.0 CG A:ASP185 3.3 16.4 1.0 CD A:GLU177 3.3 13.6 1.0 CD A:GLU190 3.3 11.2 1.0 C A:ASN183 3.6 15.7 1.0 OD1 A:ASP185 3.7 12.8 1.0 CG A:GLU190 3.8 9.9 1.0 CA A:CA323 3.8 10.9 1.0 OE1 A:GLU177 3.8 10.8 1.0 OD2 A:ASP191 4.0 17.1 1.0 N A:ASP185 4.1 11.6 1.0 CB A:ASN183 4.2 14.5 1.0 CA A:PRO184 4.2 11.2 1.0 OD1 A:ASP191 4.2 16.7 1.0 CG A:GLU177 4.3 8.9 1.0 OE1 A:GLU190 4.3 11.4 1.0 C A:PRO184 4.3 19.4 1.0 N A:PRO184 4.4 15.2 1.0 O A:LYS182 4.4 24.1 1.0 CG A:ASP191 4.4 17.3 1.0 CB A:ASP185 4.5 12.2 1.0 CA A:ASN183 4.6 13.4 1.0 CA A:ASP185 4.9 9.7 1.0 O A:PRO184 5.0 17.5 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:Ca325 b:11.0 occ:1.00 O A:HOH2239 2.3 9.6 1.0 O A:GLN61 2.3 9.1 1.0 O A:HOH2191 2.4 11.7 1.0 OD1 A:ASP57 2.4 8.7 1.0 O A:HOH2122 2.4 11.6 1.0 OD1 A:ASP59 2.5 11.2 1.0 OD2 A:ASP57 2.6 10.3 1.0 CG A:ASP57 2.8 6.6 1.0 C A:GLN61 3.5 7.0 1.0 CG A:ASP59 3.5 12.6 1.0 OD2 A:ASP59 3.9 12.5 1.0 O A:HOH2102 4.0 12.8 1.0 N A:GLN61 4.0 10.4 1.0 CA A:GLN61 4.1 7.7 1.0 N A:ASP59 4.3 10.2 1.0 CB A:ASP57 4.3 7.3 1.0 CB A:GLN61 4.3 8.7 1.0 O A:HOH2204 4.4 18.8 1.0 O A:HOH2007 4.4 11.2 1.0 N A:PHE62 4.5 7.0 1.0 O A:HOH2206 4.6 33.6 1.0 O A:HOH2003 4.6 10.0 1.0 OD2 A:ASP67 4.6 12.2 1.0 N A:ASN60 4.7 10.1 1.0 CB A:ASP59 4.7 10.3 1.0 N A:ALA58 4.7 8.8 1.0 O A:HOH2210 4.8 25.8 1.0 CA A:PHE62 4.8 5.6 1.0 CA A:ASP59 4.8 10.3 1.0 C A:ASP59 4.9 16.5 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:Ca326 b:13.9 occ:1.00 O A:TYR193 2.3 14.0 1.0 O A:ILE197 2.4 15.1 1.0 O A:HOH2169 2.4 15.2 1.0 OG1 A:THR194 2.4 16.8 1.0 O A:THR194 2.4 17.5 1.0 OD1 A:ASP200 2.5 12.7 1.0 O A:HOH2182 2.5 19.1 1.0 C A:THR194 3.2 17.3 1.0 C A:TYR193 3.3 14.2 1.0 CB A:THR194 3.5 13.6 1.0 C A:ILE197 3.5 26.4 1.0 CG A:ASP200 3.5 13.4 1.0 CA A:THR194 3.6 17.1 1.0 N A:THR194 3.8 14.2 1.0 OD2 A:ASP200 3.9 13.2 1.0 CA A:ILE197 4.2 18.1 1.0 N A:ILE197 4.2 23.1 1.0 N A:PRO195 4.3 14.3 1.0 CB A:ILE197 4.3 23.6 1.0 O A:ASP200 4.5 14.1 1.0 CA A:TYR193 4.5 10.5 1.0 N A:SER198 4.5 24.1 1.0 CD2 A:TYR193 4.6 20.2 1.0 CB A:TYR193 4.7 9.9 1.0 CA A:SER198 4.7 23.3 1.0 O A:GLU190 4.7 14.2 1.0 N A:ASP200 4.7 15.0 1.0 CA A:PRO195 4.7 14.7 1.0 CG2 A:THR194 4.7 16.2 1.0 O A:HOH2151 4.7 33.3 1.0 O A:HOH2256 4.8 34.4 1.0 CB A:ASP200 4.8 11.9 1.0 C A:ASP200 4.9 17.7 1.0 CG2 A:ILE197 4.9 22.5 1.0 C A:PRO195 5.0 19.6 1.0 C A:SER198 5.0 20.7 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