Calcium in PDB 3fvp: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3fvp 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 / 1.41
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.310, 92.310, 129.477, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 19.3

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 3fvp). 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: 3fvp:
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:10.7 occ:1.00 O A:GLU187 2.3 10.7 1.0 OD2 A:ASP138 2.3 11.1 1.0 O A:HOH1479 2.4 11.0 1.0 OE1 A:GLU177 2.5 10.9 1.0 OD1 A:ASP185 2.5 11.2 1.0 OE1 A:GLU190 2.5 11.3 1.0 OE2 A:GLU190 2.5 12.3 1.0 OE2 A:GLU177 2.7 11.9 1.0 CD A:GLU190 2.9 10.3 1.0 CD A:GLU177 3.0 11.1 1.0 CG A:ASP138 3.3 10.8 1.0 C A:GLU187 3.4 9.8 1.0 CG A:ASP185 3.4 13.6 1.0 OD2 A:ASP185 3.8 13.4 1.0 CA A:CA318 3.8 13.8 1.0 CB A:ASP138 4.0 9.2 1.0 O A:ASP185 4.1 11.5 1.0 N A:GLU187 4.2 13.1 1.0 OD1 A:ASP138 4.2 13.4 1.0 N A:ILE188 4.3 9.9 1.0 CA A:GLU187 4.3 10.7 1.0 CA A:ILE188 4.3 9.9 1.0 CG A:GLU190 4.3 12.9 1.0 CG A:GLU177 4.4 11.1 1.0 O A:HOH1431 4.4 15.3 1.0 N A:GLY189 4.4 10.2 1.0 CB A:GLU187 4.6 13.8 1.0 C A:ASP185 4.6 12.1 1.0 CB A:ASP185 4.7 12.8 1.0 N A:ASP185 4.7 11.3 1.0 C A:ILE188 4.8 8.7 1.0 CB A:GLU177 4.9 9.9 1.0 O A:HOH1599 4.9 16.5 1.0 CA A:ASP185 4.9 12.3 1.0 N A:GLU190 4.9 12.6 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:13.8 occ:1.00 O A:ASN183 2.2 13.1 1.0 OD2 A:ASP185 2.3 13.4 1.0 O A:HOH1570 2.3 17.3 1.0 O A:HOH1599 2.3 16.5 1.0 OE2 A:GLU190 2.4 12.3 1.0 OE2 A:GLU177 2.4 11.9 1.0 CG A:ASP185 3.2 13.6 1.0 CD A:GLU177 3.2 11.1 1.0 CD A:GLU190 3.4 10.3 1.0 C A:ASN183 3.5 13.7 1.0 OD1 A:ASP185 3.6 11.2 1.0 OE1 A:GLU177 3.7 10.9 1.0 CA A:CA317 3.8 10.7 1.0 CG A:GLU190 3.8 12.9 1.0 CA A:PRO184 4.1 12.4 1.0 O A:HOH1579 4.1 40.7 1.0 N A:ASP185 4.2 11.3 1.0 CB A:ASN183 4.2 15.7 1.0 OD2 A:ASP191 4.2 18.1 1.0 N A:PRO184 4.2 12.7 1.0 C A:PRO184 4.2 15.4 1.0 OD1 A:ASP191 4.2 16.2 1.0 CG A:GLU177 4.3 11.1 1.0 OE1 A:GLU190 4.3 11.3 1.0 CB A:ASP185 4.4 12.8 1.0 O A:LYS182 4.4 20.9 1.0 CA A:ASN183 4.5 14.3 1.0 CG A:ASP191 4.5 13.7 1.0 CA A:ASP185 4.9 12.3 1.0 O A:PRO184 4.9 16.4 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:11.4 occ:1.00 O A:HOH1530 2.3 14.1 1.0 O A:GLN61 2.3 10.7 1.0 O A:HOH1602 2.4 13.6 1.0 OD1 A:ASP57 2.4 11.8 1.0 OD1 A:ASP59 2.4 11.6 1.0 O A:HOH1601 2.4 12.7 1.0 OD2 A:ASP57 2.6 10.9 1.0 CG A:ASP57 2.8 8.8 1.0 CG A:ASP59 3.4 12.6 1.0 C A:GLN61 3.5 9.8 1.0 OD2 A:ASP59 3.7 16.2 1.0 N A:GLN61 3.9 10.2 1.0 O A:HOH1477 4.0 16.2 1.0 CA A:GLN61 4.1 10.4 1.0 CB A:GLN61 4.3 12.1 1.0 N A:ASP59 4.3 11.4 1.0 CB A:ASP57 4.3 10.4 1.0 O A:HOH1433 4.4 14.0 1.0 O A:HOH1600 4.5 21.7 1.0 N A:PHE62 4.5 10.2 1.0 O A:HOH1631 4.6 37.4 1.0 OD2 A:ASP67 4.6 10.4 1.0 O A:HOH1404 4.6 11.9 1.0 CB A:ASP59 4.6 12.2 1.0 N A:ASN60 4.6 10.8 1.0 O A:HOH1588 4.7 33.9 1.0 N A:ALA58 4.8 10.9 1.0 CA A:PHE62 4.8 9.1 1.0 CA A:ASP59 4.8 11.2 1.0 C A:ASP59 4.9 9.7 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:13.6 occ:1.00 O A:ILE197 2.3 16.3 1.0 O A:THR194 2.3 17.0 1.0 O A:TYR193 2.4 13.8 1.0 OG1 A:THR194 2.4 16.9 1.0 OD1 A:ASP200 2.4 13.7 1.0 O A:HOH1604 2.4 21.6 1.0 O A:HOH1589 2.4 17.6 1.0 C A:THR194 3.2 15.4 1.0 C A:TYR193 3.4 12.6 1.0 CG A:ASP200 3.4 13.6 1.0 CB A:THR194 3.5 15.5 1.0 C A:ILE197 3.5 17.3 1.0 CA A:THR194 3.7 14.7 1.0 OD2 A:ASP200 3.8 17.7 1.0 N A:THR194 3.9 13.7 1.0 CA A:ILE197 4.2 20.3 1.0 N A:PRO195 4.2 15.6 1.0 CB A:ILE197 4.3 22.1 1.0 N A:ILE197 4.3 20.6 1.0 O A:ASP200 4.5 16.6 1.0 N A:SER198 4.5 21.3 1.0 CA A:TYR193 4.6 12.1 1.0 CA A:SER198 4.6 21.5 1.0 O A:GLU190 4.6 14.2 1.0 N A:ASP200 4.6 15.6 1.0 CA A:PRO195 4.7 17.8 1.0 CB A:TYR193 4.7 13.3 1.0 CD2 A:TYR193 4.7 16.2 1.0 CG2 A:THR194 4.7 18.1 1.0 O A:HOH1603 4.8 29.5 1.0 CB A:ASP200 4.8 16.3 1.0 CG2 A:ILE197 4.8 23.0 1.0 C A:ASP200 4.9 14.1 1.0 C A:SER198 4.9 21.4 1.0 N A:GLY199 5.0 17.9 1.0 CA A:ASP200 5.0 16.1 1.0

L.Englert, A.Biela, M.Zayed, D.Hangauer, A.Heine, G.Klebe. Thermolysin Inhibition To Be Published.