Calcium in PDB 3f2p: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3f2p 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 / 1.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.787, 92.787, 130.655, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 26.2

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 3f2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Thermolysin Inhibition, PDB code: 3f2p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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:Ca2001 b:20.4 occ:1.00 O A:GLU187 2.3 18.3 1.0 OD2 A:ASP138 2.4 23.0 1.0 OD1 A:ASP185 2.4 17.8 1.0 OE2 A:GLU190 2.4 21.9 1.0 OE1 A:GLU177 2.4 18.1 1.0 O A:HOH9112 2.5 14.6 1.0 OE1 A:GLU190 2.6 22.9 1.0 OE2 A:GLU177 2.7 23.0 1.0 CD A:GLU190 2.8 16.4 1.0 CD A:GLU177 2.9 21.1 1.0 CG A:ASP185 3.3 16.8 1.0 C A:GLU187 3.4 22.3 1.0 CG A:ASP138 3.4 25.5 1.0 OD2 A:ASP185 3.6 34.1 1.0 CB A:ASP138 4.0 18.2 1.0 O A:ASP185 4.1 21.6 1.0 N A:ILE188 4.2 19.6 1.0 CA A:ILE188 4.2 23.4 1.0 N A:GLU187 4.3 22.1 1.0 CA A:GLU187 4.3 22.4 1.0 CG A:GLU177 4.4 12.2 1.0 CG A:GLU190 4.4 19.6 1.0 OD1 A:ASP138 4.4 20.4 1.0 N A:GLY189 4.4 22.7 1.0 O A:HOH9062 4.4 26.5 1.0 O A:HOH9111 4.6 27.9 1.0 C A:ASP185 4.7 22.8 1.0 CB A:ASP185 4.7 18.5 1.0 C A:ILE188 4.7 26.2 1.0 CB A:GLU187 4.7 22.1 1.0 N A:ASP185 4.8 22.0 1.0 N A:GLU190 4.9 16.2 1.0 CB A:GLU177 4.9 14.3 1.0

Calcium binding site 2 out of 3 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:Ca2003 b:17.6 occ:1.00 O A:HOH9114 2.3 16.7 1.0 O A:GLN61 2.3 19.7 1.0 OD2 A:ASP57 2.3 15.5 1.0 OD1 A:ASP57 2.4 17.8 1.0 O A:HOH9115 2.4 18.7 1.0 OD1 A:ASP59 2.5 22.3 1.0 O A:HOH9113 2.5 18.6 1.0 CG A:ASP57 2.7 17.1 1.0 CG A:ASP59 3.5 23.8 1.0 C A:GLN61 3.5 15.9 1.0 OD2 A:ASP59 3.9 21.8 1.0 O A:HOH9109 3.9 24.2 1.0 N A:GLN61 4.0 15.4 1.0 CA A:GLN61 4.2 14.1 1.0 CB A:ASP57 4.2 15.1 1.0 N A:ASP59 4.3 22.2 1.0 O A:HOH9040 4.3 19.4 1.0 CB A:GLN61 4.4 16.2 1.0 N A:PHE62 4.5 12.7 1.0 O A:HOH9006 4.6 19.1 1.0 O A:HOH9123 4.6 23.3 1.0 N A:ASN60 4.6 13.2 1.0 N A:ALA58 4.7 14.2 1.0 CB A:ASP59 4.7 14.4 1.0 OD2 A:ASP67 4.7 21.4 1.0 O A:HOH9129 4.7 33.1 1.0 CA A:PHE62 4.7 14.4 1.0 CA A:ASP59 4.8 16.5 1.0 C A:ASP59 4.9 18.7 1.0 CA A:ASP57 5.0 19.5 1.0

Calcium binding site 3 out of 3 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:Ca2004 b:24.4 occ:1.00 O A:TYR193 2.2 19.0 1.0 OG1 A:THR194 2.3 21.3 1.0 OD1 A:ASP200 2.4 17.6 1.0 O A:HOH9116 2.4 29.6 1.0 O A:THR194 2.4 25.3 1.0 O A:ILE197 2.4 31.7 1.0 O A:HOH9117 2.5 23.1 1.0 C A:THR194 3.2 30.5 1.0 C A:TYR193 3.2 23.4 1.0 CG A:ASP200 3.4 18.8 1.0 CB A:THR194 3.5 22.2 1.0 C A:ILE197 3.6 32.9 1.0 CA A:THR194 3.7 25.4 1.0 OD2 A:ASP200 3.7 24.2 1.0 N A:THR194 3.8 23.6 1.0 N A:PRO195 4.2 27.8 1.0 N A:ILE197 4.3 37.5 1.0 CA A:ILE197 4.3 34.8 1.0 O A:HOH9103 4.4 32.2 1.0 CA A:TYR193 4.4 17.9 1.0 CB A:ILE197 4.5 34.5 1.0 CD2 A:TYR193 4.6 24.1 1.0 O A:ASP200 4.6 25.6 1.0 CB A:TYR193 4.6 15.1 1.0 O A:GLU190 4.6 22.5 1.0 CG2 A:THR194 4.6 22.9 1.0 N A:SER198 4.6 34.0 1.0 N A:ASP200 4.6 24.5 1.0 CA A:PRO195 4.7 28.4 1.0 CA A:SER198 4.7 36.0 1.0 CB A:ASP200 4.7 16.9 1.0 C A:ASP200 4.8 23.6 1.0 CG A:TYR193 4.9 22.5 1.0 C A:PRO195 5.0 31.5 1.0 CA A:ASP200 5.0 20.5 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