Calcium in PDB 5uu8: Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant:
3.4.24.27;

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant, PDB code: 5uu8 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)	20.30 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.500, 97.500, 107.920, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28.9

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 30% Xylose As Cryoprotectant (pdb code 5uu8). 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 30% Xylose As Cryoprotectant, PDB code: 5uu8:
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 30% 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 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.9 occ:1.00 O A:HOH542 2.3 16.2 1.0 O A:GLU187 2.3 13.9 1.0 OE1 A:GLU177 2.3 20.7 1.0 OD2 A:ASP138 2.6 11.8 1.0 OE1 A:GLU190 2.6 20.6 1.0 OE2 A:GLU190 2.7 22.9 1.0 OD1 A:ASP185 2.7 39.2 1.0 CD A:GLU190 3.0 20.0 1.0 CD A:GLU177 3.0 18.0 1.0 OE2 A:GLU177 3.1 22.0 1.0 C A:GLU187 3.3 21.7 1.0 HA A:ILE188 3.4 14.5 1.0 CG A:ASP138 3.4 23.7 1.0 HB3 A:ASP138 3.4 29.9 1.0 CG A:ASP185 3.5 30.2 1.0 OD2 A:ASP185 3.7 23.1 1.0 H A:GLU187 3.8 24.9 1.0 H A:GLY189 3.8 25.5 1.0 ZN A:ZN402 3.8 26.8 1.0 CB A:ASP138 3.9 24.9 1.0 HD13 A:ILE188 4.0 19.3 1.0 N A:ILE188 4.1 14.8 1.0 HB2 A:ASP138 4.1 29.9 1.0 CA A:ILE188 4.1 12.1 1.0 H A:GLU190 4.1 28.2 1.0 HB2 A:GLU187 4.2 40.3 1.0 N A:GLU187 4.2 20.8 1.0 CA A:GLU187 4.3 27.3 1.0 OD1 A:ASP138 4.4 30.6 1.0 N A:GLY189 4.4 21.3 1.0 O A:HOH535 4.4 30.6 1.0 H A:ASP185 4.4 22.7 1.0 CG A:GLU177 4.5 15.7 1.0 CG A:GLU190 4.5 15.8 1.0 O A:ASP185 4.6 23.9 1.0 C A:ILE188 4.6 16.3 1.0 HB2 A:GLU177 4.7 19.7 1.0 HA A:THR174 4.7 24.7 1.0 O A:HOH505 4.7 19.1 1.0 CB A:GLU187 4.7 33.5 1.0 HG23 A:THR174 4.8 19.8 1.0 HG3 A:GLU190 4.8 19.0 1.0 HB3 A:GLU177 4.8 19.7 1.0 C A:ASP185 4.8 23.1 1.0 H A:ILE188 4.8 17.8 1.0 CB A:ASP185 4.9 22.8 1.0 CB A:GLU177 4.9 16.4 1.0 CD1 A:ILE188 4.9 16.1 1.0 HG3 A:GLU177 4.9 18.9 1.0 N A:GLU190 5.0 23.5 1.0 OG1 A:THR174 5.0 19.3 1.0 HG2 A:GLU190 5.0 19.0 1.0 N A:ASP185 5.0 18.9 1.0 HB3 A:GLU190 5.0 17.5 1.0 HG2 A:GLU177 5.0 18.9 1.0

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.5 occ:1.00 OD1 A:ASP59 2.2 30.2 1.0 O A:GLN61 2.3 26.9 1.0 O A:HOH565 2.3 23.0 1.0 OD1 A:ASP57 2.4 20.6 1.0 OD2 A:ASP57 2.5 32.8 1.0 O A:HOH617 2.6 29.4 1.0 CG A:ASP57 2.8 18.9 1.0 H A:GLN61 3.2 46.5 0.7 H A:GLN61 3.2 46.5 0.3 CG A:ASP59 3.3 32.6 1.0 C A:GLN61 3.4 32.6 1.0 H A:ASP59 3.4 40.8 1.0 HB2 A:GLN61 3.5 43.2 0.3 HB2 A:GLN61 3.5 52.5 0.7 O A:HOH594 3.6 21.5 1.0 OD2 A:ASP59 3.6 31.8 1.0 H A:ALA58 3.9 32.8 1.0 N A:GLN61 3.9 38.8 1.0 CA A:GLN61 4.0 35.5 0.3 CA A:GLN61 4.0 37.1 0.7 HA A:PHE62 4.2 38.0 1.0 CB A:GLN61 4.2 36.0 0.3 CB A:GLN61 4.2 43.7 0.7 N A:ASP59 4.3 34.0 1.0 CB A:ASP57 4.3 16.9 1.0 H A:ASN60 4.5 40.2 1.0 N A:ALA58 4.5 27.3 1.0 N A:PHE62 4.5 29.7 1.0 O A:HOH604 4.5 22.3 1.0 CB A:ASP59 4.6 32.8 1.0 OD2 A:ASP67 4.6 21.5 1.0 HB2 A:ASP57 4.7 20.2 1.0 N A:ASN60 4.7 33.5 1.0 HB3 A:GLN61 4.7 52.5 0.7 HB3 A:ASP57 4.7 20.2 1.0 HB3 A:ALA58 4.7 35.4 1.0 HA A:ASP57 4.7 27.4 1.0 HB3 A:GLN61 4.8 43.2 0.3 CA A:ASP59 4.8 33.1 1.0 CA A:PHE62 4.8 31.7 1.0 H A:PHE63 4.9 41.6 1.0 C A:ASP59 4.9 34.5 1.0 HB3 A:ASP59 4.9 39.3 1.0 CA A:ASP57 5.0 22.9 1.0 HA A:GLN61 5.0 42.6 0.3 HA A:GLN61 5.0 44.5 0.7

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 30% 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 30% Xylose As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:28.2 occ:1.00 O A:TYR193 2.2 21.9 1.0 O A:HOH504 2.4 22.1 1.0 OD1 A:ASP200 2.4 38.1 1.0 OG1 A:THR194 2.4 27.8 1.0 O A:ILE197 2.4 43.1 1.0 O A:THR194 2.4 31.3 1.0 C A:TYR193 3.3 27.9 1.0 C A:THR194 3.3 26.0 1.0 CG A:ASP200 3.3 36.7 1.0 HB A:ILE197 3.4 43.1 1.0 C A:ILE197 3.5 43.2 1.0 CB A:THR194 3.5 24.1 1.0 OD2 A:ASP200 3.6 35.9 1.0 CA A:THR194 3.8 22.1 1.0 HB A:THR194 3.8 28.9 1.0 H A:ILE197 3.8 55.4 1.0 H A:ASP200 3.9 39.8 1.0 N A:THR194 3.9 28.6 1.0 HA A:SER198 4.0 62.7 1.0 HD2 A:TYR193 4.0 29.6 1.0 HB3 A:TYR193 4.0 32.8 1.0 O A:ASP200 4.1 16.4 1.0 CB A:ILE197 4.2 35.9 1.0 CA A:ILE197 4.3 41.0 1.0 HA A:PRO195 4.3 42.9 1.0 O A:GLU190 4.3 23.0 1.0 N A:PRO195 4.4 22.2 1.0 HG22 A:ILE197 4.4 38.1 1.0 N A:ILE197 4.4 46.2 1.0 N A:SER198 4.4 51.0 1.0 CA A:TYR193 4.4 26.7 1.0 C A:ASP200 4.5 17.0 1.0 CA A:SER198 4.6 52.2 1.0 N A:ASP200 4.6 33.2 1.0 CB A:TYR193 4.6 27.3 1.0 CD2 A:TYR193 4.6 24.6 1.0 CB A:ASP200 4.6 31.2 1.0 H A:TYR193 4.7 33.3 1.0 HA A:THR194 4.7 26.5 1.0 CA A:PRO195 4.7 35.7 1.0 H A:THR194 4.8 34.3 1.0 CG2 A:THR194 4.8 22.4 1.0 CG2 A:ILE197 4.8 31.8 1.0 HG23 A:THR194 4.8 26.9 1.0 N A:TYR193 4.8 27.8 1.0 CA A:ASP200 4.8 26.1 1.0 HA A:GLU190 4.9 22.3 1.0 H A:GLY199 4.9 49.2 1.0 O A:HOH583 4.9 33.0 1.0 HA A:SER201 5.0 30.7 1.0 C A:PRO195 5.0 46.4 1.0 HG21 A:THR194 5.0 26.9 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