Calcium in PDB 5uu9: Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant:
3.4.24.27;

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant, PDB code: 5uu9 was solved by D.H.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.99 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.819, 96.819, 106.900, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.8

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant (pdb code 5uu9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant, PDB code: 5uu9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:6.8 occ:0.89 O A:GLU187 2.3 14.2 1.0 OD2 A:ASP138 2.3 12.7 1.0 O A:HOH642 2.4 12.9 1.0 OE1 A:GLU177 2.4 14.0 1.0 OE1 A:GLU190 2.4 13.7 1.0 OD1 A:ASP185 2.5 14.2 1.0 OE2 A:GLU190 2.5 13.9 1.0 OE2 A:GLU177 2.8 13.7 1.0 CD A:GLU190 2.8 12.6 1.0 CD A:GLU177 2.9 14.6 1.0 CG A:ASP138 3.3 15.3 1.0 C A:GLU187 3.4 12.6 1.0 CG A:ASP185 3.5 16.4 1.0 HA A:ILE188 3.5 16.1 1.0 HB3 A:ASP138 3.6 15.7 1.0 ZN A:ZN402 3.6 10.3 0.8 H A:GLY189 3.7 16.4 1.0 OD2 A:ASP185 3.8 15.7 1.0 H A:GLU187 3.8 17.9 0.4 H A:GLU187 3.8 17.9 0.6 HB2 A:GLU187 3.9 19.2 0.6 CB A:ASP138 4.0 13.1 1.0 H A:GLU190 4.2 17.2 1.0 N A:ILE188 4.2 14.1 1.0 O A:ASP185 4.2 14.5 1.0 HD13 A:ILE188 4.2 16.9 1.0 HB2 A:GLU187 4.2 20.5 0.4 OD1 A:ASP138 4.2 14.2 1.0 CA A:ILE188 4.2 13.4 1.0 HB2 A:ASP138 4.2 15.7 1.0 N A:GLU187 4.3 14.9 1.0 CA A:GLU187 4.3 13.9 0.6 CG A:GLU190 4.3 13.9 1.0 CA A:GLU187 4.3 14.4 0.4 H A:ASP185 4.4 17.5 1.0 CG A:GLU177 4.4 12.7 1.0 N A:GLY189 4.4 13.6 1.0 O A:HOH538 4.5 14.3 1.0 HG3 A:GLU190 4.6 16.7 1.0 CB A:GLU187 4.6 16.1 0.6 O A:HOH620 4.6 15.0 1.0 C A:ASP185 4.6 13.4 1.0 HB2 A:GLU177 4.7 15.5 1.0 C A:ILE188 4.7 14.3 1.0 HB3 A:GLU177 4.8 15.5 1.0 CB A:ASP185 4.8 13.8 1.0 CB A:GLU187 4.8 17.1 0.4 HG2 A:GLU190 4.8 16.7 1.0 HA A:THR174 4.8 15.2 1.0 N A:ASP185 4.8 14.6 1.0 HG2 A:GLU177 4.8 15.2 1.0 HG3 A:GLU177 4.9 15.2 1.0 CB A:GLU177 4.9 12.9 1.0 H A:ILE188 5.0 16.9 1.0 HB3 A:GLU190 5.0 17.2 1.0 OG1 A:THR174 5.0 13.6 1.0 N A:GLU190 5.0 14.4 1.0 HA A:PRO184 5.0 17.6 1.0

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:10.2 occ:1.00 O A:GLN61 2.2 19.8 1.0 O A:HOH788 2.2 18.2 1.0 OD1 A:ASP57 2.2 19.8 1.0 OD1 A:ASP59 2.3 21.2 1.0 O A:HOH591 2.3 21.5 1.0 O A:HOH629 2.3 19.1 1.0 OD2 A:ASP57 2.8 24.6 1.0 CG A:ASP57 2.8 20.1 1.0 H A:GLN61 3.3 21.4 0.3 H A:GLN61 3.3 21.4 0.7 CG A:ASP59 3.3 21.3 1.0 C A:GLN61 3.4 18.4 1.0 H A:ASP59 3.5 22.1 1.0 HB2 A:GLN61 3.5 25.0 0.3 HB2 A:GLN61 3.6 25.7 0.7 OD2 A:ASP59 3.7 22.4 1.0 N A:GLN61 3.9 17.9 1.0 O A:HOH735 4.0 22.1 1.0 HA A:PHE62 4.0 21.6 1.0 CA A:GLN61 4.1 18.4 0.7 CA A:GLN61 4.1 18.7 0.3 H A:ALA58 4.2 19.2 1.0 CB A:GLN61 4.3 20.8 0.3 CB A:GLN61 4.3 21.4 0.7 N A:ASP59 4.3 18.4 1.0 CB A:ASP57 4.3 17.8 1.0 N A:PHE62 4.5 17.9 1.0 H A:ASN60 4.5 23.0 1.0 O A:HOH908 4.5 45.6 1.0 O A:HOH869 4.5 26.5 1.0 OD2 A:ASP67 4.5 17.7 1.0 O A:HOH578 4.5 17.3 1.0 CB A:ASP59 4.6 19.1 1.0 N A:ALA58 4.6 16.0 1.0 HB2 A:ASP57 4.6 21.3 1.0 HB3 A:GLN61 4.7 25.7 0.7 N A:ASN60 4.7 19.1 1.0 CA A:PHE62 4.7 18.0 1.0 CA A:ASP59 4.8 18.4 1.0 HA A:ASP57 4.8 18.8 1.0 H A:PHE63 4.8 22.8 1.0 HB3 A:ASP57 4.8 21.3 1.0 HB3 A:ALA58 4.8 21.4 1.0 HB3 A:ASP59 4.9 22.9 1.0 C A:ASP59 4.9 20.7 1.0 HB3 A:GLN61 4.9 25.0 0.3 HG2 A:GLN61 5.0 27.2 0.3 HA A:GLN61 5.0 22.1 0.7 HA A:GLN61 5.0 22.5 0.3 CA A:ASP57 5.0 15.7 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetragonal Thermolysin Cryocooled to 100 K with 40% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:18.7 occ:1.00 O A:ILE197 2.3 27.8 1.0 OG1 A:THR194 2.3 21.8 1.0 O A:TYR193 2.3 19.5 1.0 O A:THR194 2.4 22.7 1.0 O A:HOH546 2.4 18.5 1.0 OD1 A:ASP200 2.4 21.3 1.0 O A:HOH779 2.4 22.3 1.0 C A:THR194 3.2 21.4 1.0 C A:TYR193 3.4 17.7 1.0 CB A:THR194 3.4 21.4 1.0 CG A:ASP200 3.4 20.4 1.0 C A:ILE197 3.5 29.1 1.0 HB A:ILE197 3.5 34.4 1.0 H A:ILE197 3.6 34.2 1.0 HB A:THR194 3.6 25.7 1.0 CA A:THR194 3.6 21.4 1.0 OD2 A:ASP200 3.8 20.6 1.0 N A:THR194 3.9 19.0 1.0 H A:ASP200 3.9 26.9 1.0 HA A:SER198 4.0 35.6 1.0 HD2 A:TYR193 4.2 26.8 1.0 CA A:ILE197 4.2 28.1 1.0 HB3 A:TYR193 4.2 23.4 1.0 N A:ILE197 4.2 28.5 1.0 CB A:ILE197 4.2 28.6 1.0 N A:PRO195 4.3 21.0 1.0 HA A:PRO195 4.3 26.2 1.0 O A:HOH767 4.3 39.6 1.0 O A:GLU190 4.5 16.5 1.0 HG22 A:ILE197 4.5 35.6 1.0 N A:SER198 4.5 27.5 1.0 O A:ASP200 4.5 18.9 1.0 CA A:TYR193 4.6 17.8 1.0 O A:HOH789 4.6 30.8 1.0 HA A:THR194 4.6 25.7 1.0 CA A:PRO195 4.7 21.9 1.0 CA A:SER198 4.7 29.7 1.0 CG2 A:THR194 4.7 22.1 1.0 N A:ASP200 4.7 22.4 1.0 CD2 A:TYR193 4.7 22.4 1.0 H A:THR194 4.7 22.8 1.0 O A:HOH759 4.7 44.2 1.0 CB A:ASP200 4.8 19.9 1.0 CB A:TYR193 4.8 19.5 1.0 C A:ASP200 4.8 17.6 1.0 HG23 A:THR194 4.8 26.5 1.0 H A:TYR193 4.8 20.9 1.0 H A:GLY199 4.9 33.2 1.0 HG21 A:THR194 4.9 26.5 1.0 CG2 A:ILE197 4.9 29.7 1.0 C A:PRO195 5.0 24.4 1.0 N A:TYR193 5.0 17.4 1.0 C A:SER198 5.0 27.3 1.0

D.H.Juers, C.A.Farley, C.P.Saxby, R.A.Cotter, J.K.B.Cahn, R.C.Holton-Burke, K.Harrison, Z.Wu. The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793