Calcium in PDB 6fsm: Crystal Structure of Tce-Treated Thermolysin

All present enzymatic activity of Crystal Structure of Tce-Treated Thermolysin:
3.4.24.27;

The structure of Crystal Structure of Tce-Treated Thermolysin, PDB code: 6fsm was solved by C.Pichlo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.47 / 1.39
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.948, 92.948, 129.668, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 16.2

The structure of Crystal Structure of Tce-Treated Thermolysin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Tce-Treated Thermolysin (pdb code 6fsm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tce-Treated Thermolysin, PDB code: 6fsm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Tce-Treated Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tce-Treated Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:13.8 occ:1.00 OD2 A:ASP138 2.3 13.4 1.0 O A:GLU187 2.3 13.4 1.0 O A:HOH599 2.4 14.5 1.0 OD1 A:ASP185 2.4 16.1 1.0 OE2 A:GLU190 2.5 15.7 1.0 OE1 A:GLU177 2.5 14.0 1.0 OE1 A:GLU190 2.5 14.4 1.0 OE2 A:GLU177 2.7 14.9 1.0 CD A:GLU190 2.8 14.1 1.0 CD A:GLU177 2.9 13.0 1.0 CG A:ASP138 3.3 12.9 1.0 C A:GLU187 3.4 14.8 1.0 CG A:ASP185 3.5 14.7 1.0 HB3 A:ASP138 3.6 14.1 1.0 HA A:ILE188 3.7 14.8 1.0 H A:GLU187 3.7 19.8 1.0 H A:GLY189 3.8 15.2 1.0 OD2 A:ASP185 3.8 19.5 1.0 CA A:CA403 3.8 19.4 1.0 HB2 A:GLU187 3.9 19.3 1.0 CB A:ASP138 4.0 11.8 1.0 H A:ASP185 4.1 18.6 1.0 O A:ASP185 4.1 14.9 1.0 H A:GLU190 4.1 16.6 1.0 N A:GLU187 4.2 16.5 1.0 HB2 A:ASP138 4.2 14.1 1.0 OD1 A:ASP138 4.2 15.6 1.0 N A:ILE188 4.2 12.2 1.0 O A:HOH587 4.3 19.5 1.0 CA A:GLU187 4.3 16.8 1.0 CG A:GLU190 4.3 16.6 1.0 CA A:ILE188 4.3 12.4 1.0 HD13 A:ILE188 4.4 21.8 1.0 CG A:GLU177 4.4 13.4 1.0 N A:GLY189 4.4 12.7 1.0 C A:ASP185 4.5 14.4 1.0 CB A:GLU187 4.6 16.1 1.0 HG3 A:GLU190 4.6 20.0 1.0 HB2 A:GLU177 4.7 17.2 1.0 O A:HOH517 4.7 23.3 1.0 N A:ASP185 4.7 15.5 1.0 CB A:ASP185 4.8 15.5 1.0 HB3 A:GLU177 4.8 17.2 1.0 HG2 A:GLU190 4.8 20.0 1.0 C A:ILE188 4.8 14.6 1.0 HG2 A:GLU177 4.8 16.1 1.0 HG3 A:GLU177 4.9 16.1 1.0 HA A:THR174 4.9 14.2 1.0 CB A:GLU177 4.9 14.4 1.0 N A:GLU190 4.9 13.8 1.0 CA A:ASP185 5.0 13.7 1.0 HB3 A:GLU190 5.0 17.4 1.0 HB3 A:GLU187 5.0 19.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tce-Treated Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tce-Treated Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:19.4 occ:1.00 O A:HOH604 2.3 21.7 1.0 O A:ASN183 2.3 22.7 1.0 OE2 A:GLU190 2.4 15.7 1.0 OD2 A:ASP185 2.4 19.5 1.0 O A:HOH517 2.4 23.3 1.0 OE2 A:GLU177 2.6 14.9 1.0 CG A:ASP185 3.3 14.7 1.0 CD A:GLU177 3.3 13.0 1.0 CD A:GLU190 3.3 14.1 1.0 C A:ASN183 3.5 22.4 1.0 HA A:PRO184 3.5 20.2 1.0 HG3 A:GLU190 3.5 20.0 1.0 OD1 A:ASP185 3.6 16.1 1.0 HB2 A:ASN183 3.7 30.4 1.0 OE1 A:GLU177 3.8 14.0 1.0 HG2 A:GLU190 3.8 20.0 1.0 CG A:GLU190 3.8 16.6 1.0 CA A:CA402 3.8 13.8 1.0 HB3 A:ASN183 3.8 30.4 1.0 H A:ASP185 4.0 18.6 1.0 CA A:PRO184 4.1 16.8 1.0 N A:ASP185 4.1 15.5 1.0 CB A:ASN183 4.1 25.3 1.0 O A:HOH731 4.2 33.7 1.0 OD1 A:ASP191 4.2 20.3 1.0 C A:PRO184 4.3 18.5 1.0 OD2 A:ASP191 4.3 21.0 1.0 N A:PRO184 4.3 18.9 1.0 HG2 A:GLU177 4.3 16.1 1.0 CG A:GLU177 4.3 13.4 1.0 OE1 A:GLU190 4.3 14.4 1.0 HB3 A:ASP185 4.3 18.6 1.0 CB A:ASP185 4.4 15.5 1.0 HG3 A:GLU177 4.4 16.1 1.0 CA A:ASN183 4.4 28.6 1.0 CG A:ASP191 4.6 22.0 1.0 H A:ASN183 4.7 33.4 1.0 CA A:ASP185 4.9 13.7 1.0 O A:PRO184 5.0 20.1 1.0 O A:HOH587 5.0 19.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tce-Treated Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tce-Treated Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:14.2 occ:1.00 O A:GLN61 2.3 14.3 1.0 O A:HOH733 2.3 19.0 1.0 OD2 A:ASP57 2.3 14.3 1.0 O A:HOH588 2.4 17.4 1.0 OD1 A:ASP59 2.4 15.8 1.0 O A:HOH589 2.4 15.2 1.0 OD1 A:ASP57 2.5 14.5 1.0 CG A:ASP57 2.8 13.9 1.0 H A:GLN61 3.3 16.6 1.0 CG A:ASP59 3.4 17.4 1.0 C A:GLN61 3.4 11.9 1.0 H A:ASP59 3.6 16.9 1.0 HB2 A:GLN61 3.6 19.1 1.0 OD2 A:ASP59 3.8 19.8 1.0 N A:GLN61 3.9 13.9 1.0 O A:HOH661 4.0 21.1 1.0 HA A:PHE62 4.0 14.0 1.0 CA A:GLN61 4.1 13.3 1.0 H A:ALA58 4.3 16.1 1.0 CB A:ASP57 4.3 13.9 1.0 CB A:GLN61 4.3 15.9 1.0 N A:ASP59 4.4 14.1 1.0 H A:ASN60 4.4 15.4 1.0 O A:HOH694 4.5 20.0 1.0 N A:PHE62 4.5 12.3 1.0 O A:HOH778 4.5 25.5 1.0 CB A:ASP59 4.6 14.3 1.0 O A:HOH527 4.6 15.2 1.0 N A:ASN60 4.7 12.9 1.0 OD2 A:ASP67 4.7 14.8 1.0 O A:HOH788 4.7 31.1 1.0 HB2 A:ASP57 4.7 16.7 1.0 N A:ALA58 4.7 13.4 1.0 HB3 A:ASP57 4.7 16.7 1.0 CA A:PHE62 4.8 11.7 1.0 CA A:ASP59 4.8 14.2 1.0 O A:HOH775 4.8 34.0 1.0 H A:PHE63 4.8 15.8 1.0 HA A:ASP57 4.8 15.7 1.0 C A:ASP59 4.9 14.3 1.0 HB3 A:GLN61 4.9 19.1 1.0 HB3 A:ASP59 4.9 17.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Tce-Treated Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tce-Treated Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:17.6 occ:1.00 O A:ILE197 2.2 19.3 1.0 O A:TYR193 2.3 16.0 1.0 O A:THR194 2.4 20.0 1.0 OG1 A:THR194 2.4 18.5 1.0 OD1 A:ASP200 2.4 19.8 1.0 O A:HOH574 2.4 18.4 1.0 O A:HOH718 2.5 23.6 1.0 C A:THR194 3.2 19.9 1.0 C A:TYR193 3.3 16.5 1.0 CB A:THR194 3.4 19.4 1.0 C A:ILE197 3.4 21.7 1.0 HB A:ILE197 3.4 37.3 1.0 CG A:ASP200 3.5 19.4 1.0 H A:ILE197 3.6 32.4 1.0 CA A:THR194 3.6 18.1 1.0 HB A:THR194 3.7 23.3 1.0 OD2 A:ASP200 3.8 21.0 1.0 N A:THR194 3.8 16.5 1.0 H A:ASP200 3.9 27.4 1.0 HA A:SER198 4.0 33.3 1.0 HD2 A:TYR193 4.0 23.6 1.0 HB3 A:TYR193 4.1 22.1 1.0 CA A:ILE197 4.2 27.9 1.0 CB A:ILE197 4.2 31.1 1.0 N A:PRO195 4.2 19.9 1.0 N A:ILE197 4.3 27.0 1.0 HA A:PRO195 4.3 24.1 1.0 HG22 A:ILE197 4.4 33.7 1.0 N A:SER198 4.5 26.1 1.0 O A:ASP200 4.5 19.2 1.0 CA A:TYR193 4.5 15.7 1.0 HA A:THR194 4.6 21.7 1.0 O A:GLU190 4.6 16.4 1.0 CA A:SER198 4.6 27.8 1.0 CD2 A:TYR193 4.6 19.7 1.0 N A:ASP200 4.6 22.8 1.0 CA A:PRO195 4.7 20.1 1.0 H A:THR194 4.7 19.8 1.0 CB A:TYR193 4.7 18.4 1.0 CG2 A:THR194 4.7 18.8 1.0 O A:HOH738 4.7 30.1 1.0 H A:GLY199 4.7 28.1 1.0 CB A:ASP200 4.8 21.4 1.0 C A:ASP200 4.8 17.7 1.0 HG23 A:THR194 4.8 22.5 1.0 CG2 A:ILE197 4.8 28.1 1.0 H A:TYR193 4.9 18.4 1.0 C A:PRO195 4.9 24.6 1.0 C A:SER198 5.0 24.2 1.0 CA A:ASP200 5.0 21.8 1.0 HG21 A:THR194 5.0 22.5 1.0 N A:GLY199 5.0 23.4 1.0

C.Pichlo, C.Toelzer, K.Chojnacki, S.Ocal, M.Uthoff, S.Ruegenberg, T.Hermanns, M.Schacherl, M.S.Denzel, K.Hofmann, K.Niefind, U.Baumann. Improved Protein-Crystal Identification By Using 2,2,2-Trichloroethanol As A Fluorescence Enhancer. Acta Crystallogr F Struct V. 74 307 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29717999
DOI: 10.1107/S2053230X18005253