Calcium in PDB 3fv4: Thermolysin Inhibition

All present enzymatic activity of Thermolysin Inhibition:
3.4.24.27;

The structure of Thermolysin Inhibition, PDB code: 3fv4 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 / 1.56
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.830, 92.830, 130.689, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.8

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 3fv4). 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: 3fv4:
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:9.5 occ:1.00 OD2 A:ASP138 2.3 9.1 1.0 O A:GLU187 2.3 9.5 1.0 OE1 A:GLU177 2.4 10.5 1.0 OE1 A:GLU190 2.5 9.0 1.0 O A:HOH1411 2.5 8.2 1.0 OE2 A:GLU190 2.5 9.6 1.0 OD1 A:ASP185 2.5 11.4 1.0 OE2 A:GLU177 2.8 9.5 1.0 CD A:GLU190 2.8 9.5 1.0 CD A:GLU177 3.0 9.8 1.0 CG A:ASP138 3.4 16.6 1.0 C A:GLU187 3.4 8.4 1.0 CG A:ASP185 3.5 14.4 1.0 CA A:CA318 3.8 12.9 1.0 OD2 A:ASP185 3.9 12.4 1.0 CB A:ASP138 4.0 7.4 1.0 O A:HOH1622 4.2 17.7 1.0 N A:GLU187 4.2 8.7 1.0 N A:ILE188 4.2 9.0 1.0 O A:ASP185 4.3 10.7 1.0 CA A:ILE188 4.3 8.3 1.0 CA A:GLU187 4.3 11.6 0.6 CA A:GLU187 4.3 11.0 0.4 CG A:GLU190 4.3 10.3 1.0 OD1 A:ASP138 4.3 14.0 1.0 N A:GLY189 4.4 9.3 1.0 CG A:GLU177 4.4 10.3 1.0 O A:HOH1451 4.6 15.7 1.0 CB A:GLU187 4.7 9.4 0.6 C A:ASP185 4.7 10.1 1.0 CB A:GLU187 4.8 11.8 0.4 C A:ILE188 4.8 9.5 1.0 N A:ASP185 4.8 9.5 1.0 CB A:ASP185 4.8 8.7 1.0 CB A:GLU177 4.9 8.4 1.0 O A:HOH1623 4.9 14.3 1.0 N A:GLU190 4.9 10.9 1.0 OG1 A:THR174 5.0 8.1 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:12.9 occ:1.00 O A:HOH1621 2.3 14.3 1.0 OE2 A:GLU190 2.3 9.6 1.0 O A:ASN183 2.3 14.2 1.0 O A:HOH1623 2.4 14.3 1.0 OD2 A:ASP185 2.4 12.4 1.0 OE2 A:GLU177 2.5 9.5 1.0 CG A:ASP185 3.2 14.4 1.0 CD A:GLU177 3.3 9.8 1.0 CD A:GLU190 3.3 9.5 1.0 C A:ASN183 3.5 14.3 1.0 OD1 A:ASP185 3.6 11.4 1.0 OE1 A:GLU177 3.7 10.5 1.0 CA A:CA317 3.8 9.5 1.0 CG A:GLU190 3.8 10.3 1.0 N A:ASP185 4.1 9.5 1.0 CA A:PRO184 4.2 8.5 1.0 CB A:ASN183 4.2 13.3 1.0 OD2 A:ASP191 4.2 13.7 1.0 OD1 A:ASP191 4.2 15.7 1.0 C A:PRO184 4.3 15.3 1.0 OE1 A:GLU190 4.3 9.0 1.0 CG A:GLU177 4.3 10.3 1.0 N A:PRO184 4.3 15.0 1.0 O A:LYS182 4.4 18.1 1.0 CB A:ASP185 4.4 8.7 1.0 CA A:ASN183 4.5 15.3 1.0 CG A:ASP191 4.5 9.9 1.0 O A:HOH1622 4.6 17.7 1.0 O A:HOH1655 4.6 42.0 1.0 CA A:ASP185 4.9 7.9 1.0 O A:PRO184 4.9 15.0 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:10.3 occ:1.00 O A:GLN61 2.3 10.1 1.0 O A:HOH1626 2.3 13.8 1.0 OD2 A:ASP57 2.4 10.2 1.0 OD1 A:ASP59 2.4 10.2 1.0 O A:HOH1464 2.4 13.1 1.0 O A:HOH1625 2.4 11.9 1.0 OD1 A:ASP57 2.5 9.4 1.0 CG A:ASP57 2.8 10.3 1.0 CG A:ASP59 3.4 15.2 1.0 C A:GLN61 3.5 10.4 1.0 OD2 A:ASP59 3.8 13.9 1.0 O A:HOH1624 3.9 16.6 1.0 N A:GLN61 4.0 10.7 1.0 CA A:GLN61 4.2 9.3 1.0 N A:ASP59 4.3 10.6 1.0 CB A:GLN61 4.3 9.4 1.0 CB A:ASP57 4.3 8.9 1.0 O A:HOH1427 4.4 13.0 1.0 N A:PHE62 4.6 8.0 1.0 O A:HOH1606 4.6 17.1 1.0 O A:HOH1414 4.6 9.7 1.0 OD2 A:ASP67 4.6 10.1 1.0 CB A:ASP59 4.7 10.2 1.0 N A:ASN60 4.7 8.7 1.0 N A:ALA58 4.7 9.7 1.0 CA A:PHE62 4.8 6.7 1.0 O A:HOH1635 4.8 29.8 1.0 CA A:ASP59 4.8 12.3 1.0 C A:ASP59 4.9 15.5 1.0 O A:HOH1576 5.0 29.1 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:Ca320 b:12.9 occ:1.00 O A:ILE197 2.3 19.9 1.0 O A:HOH1628 2.3 19.6 1.0 O A:TYR193 2.4 14.1 1.0 OD1 A:ASP200 2.4 11.8 1.0 O A:THR194 2.4 14.6 1.0 O A:HOH1574 2.4 13.6 1.0 OG1 A:THR194 2.4 13.9 1.0 C A:THR194 3.2 17.2 1.0 C A:TYR193 3.3 12.8 1.0 CG A:ASP200 3.4 13.5 1.0 CB A:THR194 3.5 13.4 1.0 C A:ILE197 3.5 19.5 1.0 CA A:THR194 3.6 13.0 1.0 OD2 A:ASP200 3.8 16.7 1.0 N A:THR194 3.8 11.7 1.0 CA A:ILE197 4.2 13.7 1.0 N A:ILE197 4.3 18.5 1.0 N A:PRO195 4.3 14.6 1.0 CB A:ILE197 4.3 24.9 1.0 N A:SER198 4.5 21.6 1.0 CA A:TYR193 4.5 10.1 1.0 O A:ASP200 4.6 15.8 1.0 CA A:SER198 4.6 27.2 1.0 O A:GLU190 4.6 11.7 1.0 O A:HOH1627 4.6 23.7 1.0 N A:ASP200 4.6 15.7 1.0 CD2 A:TYR193 4.6 14.3 1.0 CA A:PRO195 4.7 14.9 1.0 CB A:TYR193 4.7 10.3 1.0 CB A:ASP200 4.8 15.1 1.0 CG2 A:THR194 4.8 11.2 1.0 CG2 A:ILE197 4.9 25.2 1.0 C A:ASP200 4.9 13.3 1.0 C A:SER198 4.9 24.1 1.0 N A:GLY199 5.0 18.1 1.0 C A:PRO195 5.0 15.5 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