Calcium in PDB 3flf: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3flf 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)	10.00 / 1.97
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.658, 92.658, 130.477, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 26.5

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 3flf). 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: 3flf:
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:Ca2000 b:19.6 occ:1.00 O A:GLU187 2.3 13.8 1.0 OE2 A:GLU190 2.4 13.1 1.0 OD1 A:ASP185 2.4 19.7 1.0 OE1 A:GLU177 2.5 18.4 1.0 OD2 A:ASP138 2.5 24.4 1.0 OE1 A:GLU190 2.5 18.6 1.0 O A:HOH2268 2.6 14.9 1.0 OE2 A:GLU177 2.7 22.2 1.0 CD A:GLU190 2.8 22.8 1.0 CD A:GLU177 2.9 22.1 1.0 C A:GLU187 3.3 15.3 1.0 CG A:ASP185 3.4 19.4 1.0 CG A:ASP138 3.5 21.7 1.0 OD2 A:ASP185 3.7 18.3 1.0 CA A:CA2001 3.8 21.7 1.0 CB A:ASP138 4.0 20.0 1.0 N A:GLU187 4.2 17.4 1.0 CA A:GLU187 4.2 19.3 1.0 N A:ILE188 4.2 14.5 1.0 O A:ASP185 4.2 12.9 1.0 CA A:ILE188 4.3 16.2 1.0 CG A:GLU190 4.3 18.9 1.0 OD1 A:ASP138 4.3 19.2 1.0 CG A:GLU177 4.4 21.5 1.0 N A:GLY189 4.4 13.3 1.0 CB A:GLU187 4.5 20.5 1.0 C A:ASP185 4.6 19.5 1.0 N A:ASP185 4.6 14.2 1.0 O A:HOH2202 4.7 29.1 1.0 C A:ILE188 4.7 18.9 1.0 CB A:ASP185 4.7 16.6 1.0 N A:GLU190 4.9 17.5 1.0 CB A:GLU177 4.9 20.1 1.0 CA A:ASP185 4.9 12.8 1.0 O A:HOH2220 5.0 19.4 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:Ca2001 b:21.7 occ:1.00 O A:HOH2269 2.3 23.4 1.0 OE2 A:GLU190 2.3 13.1 1.0 OD2 A:ASP185 2.4 18.3 1.0 OE2 A:GLU177 2.4 22.2 1.0 O A:ASN183 2.4 29.9 1.0 O A:HOH2220 2.5 19.4 1.0 CD A:GLU177 3.3 22.1 1.0 CG A:ASP185 3.3 19.4 1.0 CD A:GLU190 3.3 22.8 1.0 C A:ASN183 3.6 28.2 1.0 OD1 A:ASP185 3.7 19.7 1.0 OE1 A:GLU177 3.8 18.4 1.0 CA A:CA2000 3.8 19.6 1.0 CG A:GLU190 3.8 18.9 1.0 OD1 A:ASP191 4.1 20.2 1.0 N A:ASP185 4.1 14.2 1.0 OD2 A:ASP191 4.2 22.8 1.0 CA A:PRO184 4.2 14.9 1.0 C A:PRO184 4.2 24.0 1.0 CB A:ASN183 4.3 30.1 1.0 CG A:GLU177 4.3 21.5 1.0 OE1 A:GLU190 4.3 18.6 1.0 N A:PRO184 4.4 23.2 1.0 CB A:ASP185 4.4 16.6 1.0 CG A:ASP191 4.4 17.3 1.0 O A:LYS182 4.5 32.1 1.0 CA A:ASN183 4.6 30.2 1.0 O A:PRO184 4.9 28.4 1.0 CA A:ASP185 4.9 12.8 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:Ca2002 b:19.2 occ:1.00 O A:GLN61 2.3 16.6 1.0 O A:HOH2271 2.3 20.8 1.0 O A:HOH2270 2.3 14.2 1.0 OD1 A:ASP59 2.4 21.0 1.0 OD2 A:ASP57 2.5 13.0 1.0 O A:HOH2281 2.5 18.9 1.0 OD1 A:ASP57 2.5 16.5 1.0 CG A:ASP57 2.8 14.8 1.0 CG A:ASP59 3.4 20.8 1.0 C A:GLN61 3.4 16.3 1.0 OD2 A:ASP59 3.7 20.9 1.0 O A:HOH2194 3.8 24.1 1.0 N A:GLN61 3.9 17.8 1.0 CA A:GLN61 4.1 17.5 1.0 CB A:GLN61 4.2 15.7 1.0 O A:HOH2302 4.2 42.3 1.0 N A:ASP59 4.3 17.8 1.0 CB A:ASP57 4.3 11.0 1.0 O A:HOH2131 4.4 16.1 1.0 O A:HOH2108 4.5 15.5 1.0 N A:PHE62 4.5 11.8 1.0 OD2 A:ASP67 4.6 18.4 1.0 N A:ASN60 4.7 16.7 1.0 CB A:ASP59 4.7 16.7 1.0 N A:ALA58 4.7 14.9 1.0 O A:HOH2298 4.7 42.2 1.0 CA A:PHE62 4.7 15.0 1.0 CA A:ASP59 4.8 17.0 1.0 C A:ASP59 4.9 16.8 1.0 O A:HOH2293 4.9 31.1 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:Ca2003 b:22.8 occ:1.00 O A:ILE197 2.3 19.8 1.0 O A:TYR193 2.3 19.2 1.0 O A:HOH2273 2.3 17.3 1.0 OG1 A:THR194 2.4 21.5 1.0 O A:THR194 2.4 23.7 1.0 OD1 A:ASP200 2.4 25.8 1.0 O A:HOH2272 2.6 21.0 1.0 C A:THR194 3.2 20.4 1.0 C A:TYR193 3.3 20.2 1.0 CG A:ASP200 3.4 21.1 1.0 C A:ILE197 3.4 25.5 1.0 CB A:THR194 3.4 22.1 1.0 OD2 A:ASP200 3.6 24.3 1.0 CA A:THR194 3.6 20.0 1.0 N A:THR194 3.8 17.6 1.0 CA A:ILE197 4.1 25.6 1.0 N A:ILE197 4.1 32.7 1.0 CB A:ILE197 4.2 32.6 1.0 N A:PRO195 4.3 20.3 1.0 O A:ASP200 4.3 21.5 1.0 CA A:TYR193 4.5 21.6 1.0 N A:SER198 4.5 24.4 1.0 CD2 A:TYR193 4.5 18.2 1.0 N A:ASP200 4.6 20.4 1.0 CB A:TYR193 4.7 20.1 1.0 CG2 A:THR194 4.7 21.7 1.0 O A:GLU190 4.7 18.0 1.0 CA A:SER198 4.7 29.4 0.6 CA A:SER198 4.7 29.4 0.4 O A:HOH2187 4.7 35.1 1.0 CB A:ASP200 4.7 15.7 1.0 C A:ASP200 4.8 23.0 1.0 CA A:PRO195 4.8 23.5 1.0 CG2 A:ILE197 4.9 32.7 1.0 CG A:TYR193 4.9 24.7 1.0 CA A:ASP200 5.0 15.8 1.0 C A:SER198 5.0 24.4 1.0

L.Englert, A.Biela, M.Zayed, A.Heine, D.Hangauer, G.Klebe. Displacement of Disordered Water Molecules From Hydrophobic Pocket Creates Enthalpic Signature: Binding of Phosphonamidate to the S1'-Pocket of Thermolysin. Biochim.Biophys.Acta V.1800 1192 2010.
ISSN: ISSN 0006-3002
PubMed: 20600625
DOI: 10.1016/J.BBAGEN.2010.06.009