Calcium in PDB 5uua: Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant:
3.4.24.27;

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant, PDB code: 5uua 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)	21.04 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.705, 96.705, 106.734, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.6

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant (pdb code 5uua). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Xylose As Cryoprotectant, PDB code: 5uua:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% 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 50% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.2 occ:1.00 O A:GLU187 2.3 11.7 1.0 OD2 A:ASP138 2.4 12.3 1.0 O A:HOH615 2.4 11.4 1.0 OE1 A:GLU177 2.5 12.3 1.0 OE2 A:GLU190 2.5 11.8 1.0 OD1 A:ASP185 2.5 12.2 1.0 OE1 A:GLU190 2.5 13.2 1.0 OE2 A:GLU177 2.7 12.5 1.0 CD A:GLU190 2.8 10.3 1.0 CD A:GLU177 2.9 13.2 1.0 CG A:ASP138 3.3 13.9 1.0 C A:GLU187 3.4 11.7 1.0 CG A:ASP185 3.5 15.4 1.0 HA A:ILE188 3.5 14.9 1.0 ZN A:ZN402 3.6 16.1 1.0 HB3 A:ASP138 3.6 13.3 1.0 H A:GLY189 3.8 13.6 1.0 H A:GLU187 3.8 15.9 0.6 H A:GLU187 3.8 15.9 0.4 OD2 A:ASP185 3.8 14.0 1.0 HB2 A:GLU187 3.9 16.9 0.6 CB A:ASP138 4.0 11.1 1.0 H A:GLU190 4.1 16.3 1.0 O A:ASP185 4.1 13.3 1.0 HD13 A:ILE188 4.2 15.3 1.0 N A:ILE188 4.2 13.0 1.0 OD1 A:ASP138 4.2 12.7 1.0 HB2 A:GLU187 4.2 17.7 0.4 CA A:ILE188 4.3 12.4 1.0 N A:GLU187 4.3 13.3 1.0 HB2 A:ASP138 4.3 13.3 1.0 CG A:GLU190 4.3 13.6 1.0 CA A:GLU187 4.3 12.6 0.6 H A:ASP185 4.3 15.8 1.0 CA A:GLU187 4.4 12.6 0.4 N A:GLY189 4.4 11.3 1.0 CG A:GLU177 4.4 12.0 1.0 O A:HOH542 4.5 12.6 1.0 HG3 A:GLU190 4.5 16.3 1.0 O A:HOH612 4.6 13.8 1.0 C A:ASP185 4.6 12.1 1.0 CB A:GLU187 4.6 14.1 0.6 HB2 A:GLU177 4.7 14.4 1.0 HG2 A:GLU190 4.7 16.3 1.0 CB A:ASP185 4.8 12.2 1.0 C A:ILE188 4.8 12.8 1.0 HB3 A:GLU177 4.8 14.4 1.0 N A:ASP185 4.8 13.2 1.0 HA A:THR174 4.8 13.5 1.0 CB A:GLU187 4.8 14.8 0.4 HG2 A:GLU177 4.9 14.4 1.0 HG3 A:GLU177 4.9 14.4 1.0 CB A:GLU177 4.9 12.0 1.0 HB3 A:GLU190 4.9 16.4 1.0 N A:GLU190 4.9 13.6 1.0 OG1 A:THR174 5.0 11.3 1.0 HA A:PRO184 5.0 18.5 1.0

Calcium binding site 2 out of 2 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% 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 50% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:20.8 occ:1.00 O A:ILE197 2.3 26.1 1.0 OG1 A:THR194 2.3 20.2 1.0 O A:THR194 2.4 21.1 1.0 O A:HOH557 2.4 17.5 1.0 O A:TYR193 2.4 17.6 1.0 OD1 A:ASP200 2.4 18.8 1.0 O A:HOH806 2.4 21.0 1.0 C A:THR194 3.2 19.9 1.0 C A:TYR193 3.4 16.7 1.0 HB A:ILE197 3.4 31.9 1.0 CB A:THR194 3.4 19.9 1.0 CG A:ASP200 3.5 19.0 1.0 C A:ILE197 3.5 27.2 1.0 H A:ILE197 3.6 32.2 1.0 CA A:THR194 3.7 20.6 1.0 HB A:THR194 3.7 23.9 1.0 OD2 A:ASP200 3.8 21.1 1.0 N A:THR194 3.9 18.6 1.0 H A:ASP200 3.9 25.5 1.0 HA A:SER198 4.1 32.8 1.0 HD2 A:TYR193 4.2 24.3 1.0 HB3 A:TYR193 4.2 21.4 1.0 CA A:ILE197 4.2 25.2 1.0 CB A:ILE197 4.2 26.6 1.0 N A:ILE197 4.2 26.9 1.0 N A:PRO195 4.3 19.9 1.0 HA A:PRO195 4.3 26.1 1.0 O A:HOH746 4.3 39.7 1.0 O A:GLU190 4.5 14.9 1.0 HG22 A:ILE197 4.5 33.7 1.0 O A:ASP200 4.5 17.3 1.0 N A:SER198 4.5 24.8 1.0 HA A:THR194 4.6 24.7 1.0 CA A:TYR193 4.6 15.1 1.0 O A:HOH814 4.6 28.7 1.0 O A:HOH776 4.6 46.7 1.0 CA A:PRO195 4.7 21.7 1.0 CG2 A:THR194 4.7 21.0 1.0 CA A:SER198 4.7 27.4 1.0 N A:ASP200 4.7 21.3 1.0 H A:THR194 4.7 22.3 1.0 CD2 A:TYR193 4.7 20.3 1.0 CB A:TYR193 4.8 17.8 1.0 CB A:ASP200 4.8 18.3 1.0 C A:ASP200 4.8 15.8 1.0 HG23 A:THR194 4.8 25.2 1.0 H A:TYR193 4.9 18.4 1.0 H A:GLY199 4.9 30.9 1.0 CG2 A:ILE197 4.9 28.1 1.0 HG21 A:THR194 4.9 25.2 1.0 C A:PRO195 5.0 24.0 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