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

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

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant, PDB code: 5uuc 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)	19.89 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.546, 96.546, 105.280, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 16.6

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

Zinc	(Zn)	10 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Mpd As Cryoprotectant (pdb code 5uuc). 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 50% Mpd As Cryoprotectant, PDB code: 5uuc:
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 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.4 occ:1.00 O A:GLU187 2.3 11.7 1.0 OD2 A:ASP138 2.4 12.1 1.0 O A:HOH585 2.4 11.9 1.0 OD1 A:ASP185 2.5 13.2 1.0 OE1 A:GLU177 2.5 12.8 1.0 OE2 A:GLU190 2.5 12.9 1.0 OE1 A:GLU190 2.5 12.3 1.0 OE2 A:GLU177 2.7 12.5 1.0 CD A:GLU190 2.8 11.0 1.0 CD A:GLU177 2.9 12.1 1.0 CG A:ASP138 3.4 13.6 1.0 C A:GLU187 3.4 11.2 1.0 CG A:ASP185 3.5 15.0 1.0 HA A:ILE188 3.5 14.4 1.0 HB3 A:ASP138 3.5 13.3 1.0 ZN A:ZN402 3.6 15.1 1.0 H A:GLU187 3.8 16.0 0.3 H A:GLU187 3.8 16.0 0.7 H A:GLY189 3.8 13.1 1.0 OD2 A:ASP185 3.8 13.3 1.0 HB2 A:GLU187 3.9 15.6 0.3 CB A:ASP138 4.0 11.1 1.0 O A:ASP185 4.1 13.1 1.0 H A:GLU190 4.1 15.4 1.0 HD13 A:ILE188 4.2 16.4 1.0 N A:ILE188 4.2 12.7 1.0 HB2 A:ASP138 4.2 13.3 1.0 O A:HOH666 4.2 52.4 1.0 N A:GLU187 4.2 13.3 1.0 CA A:ILE188 4.3 12.0 1.0 H A:ASP185 4.3 15.9 1.0 OD1 A:ASP138 4.3 13.9 1.0 CA A:GLU187 4.3 12.1 0.3 CG A:GLU190 4.3 12.7 1.0 CA A:GLU187 4.4 12.7 0.7 CG A:GLU177 4.4 13.1 1.0 O A:HOH575 4.4 15.8 1.0 N A:GLY189 4.4 10.9 1.0 HB2 A:GLU187 4.5 18.8 0.7 O A:HOH550 4.5 13.5 1.0 C A:ASP185 4.5 13.6 1.0 HG3 A:GLU190 4.6 15.3 1.0 CB A:GLU187 4.6 13.0 0.3 HB2 A:GLU177 4.7 15.1 1.0 CB A:ASP185 4.7 12.5 1.0 HB3 A:GLU177 4.8 15.1 1.0 C A:ILE188 4.8 12.0 1.0 N A:ASP185 4.8 13.2 1.0 HG2 A:GLU190 4.8 15.3 1.0 HG2 A:GLU177 4.8 15.8 1.0 HA A:THR174 4.8 15.5 1.0 HG3 A:GLU177 4.9 15.8 1.0 CB A:GLU177 4.9 12.6 1.0 HB2 A:ASP185 4.9 15.0 1.0 N A:GLU190 4.9 12.8 1.0 CA A:ASP185 4.9 11.6 1.0 HB3 A:GLU190 5.0 14.9 1.0 OG1 A:THR174 5.0 12.2 1.0 CB A:GLU187 5.0 15.7 0.7

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Mpd 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% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.4 occ:1.00 O A:GLN61 2.2 18.7 1.0 O A:HOH799 2.3 17.0 1.0 OD1 A:ASP57 2.3 16.7 1.0 O A:HOH656 2.3 16.8 1.0 O A:HOH576 2.4 19.8 1.0 OD1 A:ASP59 2.4 18.9 1.0 OD2 A:ASP57 2.7 19.1 1.0 CG A:ASP57 2.8 17.1 1.0 H A:GLN61 3.3 20.2 1.0 CG A:ASP59 3.4 21.3 1.0 C A:GLN61 3.4 15.9 1.0 H A:ASP59 3.5 21.6 1.0 HB2 A:GLN61 3.7 27.0 1.0 OD2 A:ASP59 3.7 21.4 1.0 O A:HOH731 3.9 21.7 1.0 N A:GLN61 4.0 16.8 1.0 HA A:PHE62 4.0 18.3 1.0 CA A:GLN61 4.1 16.9 1.0 H A:ALA58 4.2 20.8 1.0 N A:ASP59 4.3 18.0 1.0 CB A:ASP57 4.3 15.3 1.0 CB A:GLN61 4.3 22.5 1.0 H A:ASN60 4.4 22.3 1.0 N A:PHE62 4.5 17.1 1.0 O A:HOH586 4.6 15.1 1.0 OD2 A:ASP67 4.6 16.9 1.0 O A:HOH873 4.6 35.2 1.0 CB A:ASP59 4.6 19.5 1.0 HB2 A:ASP57 4.7 18.4 1.0 N A:ALA58 4.7 17.3 1.0 N A:ASN60 4.7 18.6 1.0 O A:HOH862 4.7 24.0 1.0 CA A:PHE62 4.7 15.2 1.0 H A:PHE63 4.8 19.6 1.0 HB3 A:GLN61 4.8 27.0 1.0 CA A:ASP59 4.8 19.3 1.0 HB3 A:ASP57 4.8 18.4 1.0 HA A:ASP57 4.8 18.2 1.0 C A:ASP59 4.9 20.1 1.0 HB3 A:ALA58 4.9 21.7 1.0 HB3 A:ASP59 5.0 23.4 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Mpd 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 50% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:20.6 occ:1.00 O A:ILE197 2.3 25.0 1.0 OG1 A:THR194 2.3 18.7 1.0 OD1 A:ASP200 2.3 18.0 1.0 O A:HOH584 2.4 17.7 1.0 O A:TYR193 2.4 16.6 1.0 O A:THR194 2.4 19.9 1.0 O A:HOH778 2.4 22.1 1.0 C A:THR194 3.2 20.3 1.0 C A:TYR193 3.4 16.1 1.0 CG A:ASP200 3.4 17.0 1.0 HB A:ILE197 3.4 29.3 1.0 CB A:THR194 3.5 19.9 1.0 C A:ILE197 3.5 28.6 1.0 H A:ILE197 3.6 31.7 1.0 CA A:THR194 3.7 20.2 1.0 HB A:THR194 3.8 23.9 1.0 OD2 A:ASP200 3.8 19.0 1.0 H A:ASP200 3.9 26.2 1.0 N A:THR194 3.9 17.5 1.0 HA A:SER198 4.0 32.9 1.0 HB3 A:TYR193 4.2 19.7 1.0 HD2 A:TYR193 4.2 22.7 1.0 CA A:ILE197 4.2 24.1 1.0 CB A:ILE197 4.2 24.4 1.0 HA A:PRO195 4.2 26.3 1.0 N A:ILE197 4.2 26.4 1.0 N A:PRO195 4.3 19.3 1.0 O A:HOH653 4.4 39.6 1.0 O A:ASP200 4.5 16.3 1.0 HG22 A:ILE197 4.5 30.0 1.0 N A:SER198 4.5 26.7 1.0 CA A:TYR193 4.6 15.4 1.0 O A:GLU190 4.6 15.9 1.0 O A:HOH802 4.6 34.7 1.0 HA A:THR194 4.6 24.2 1.0 CA A:PRO195 4.6 21.9 1.0 CA A:SER198 4.6 27.4 1.0 N A:ASP200 4.7 21.8 1.0 CG2 A:THR194 4.7 19.5 1.0 CB A:ASP200 4.7 17.9 1.0 H A:THR194 4.7 21.0 1.0 CB A:TYR193 4.7 16.4 1.0 CD2 A:TYR193 4.7 18.9 1.0 C A:ASP200 4.8 15.8 1.0 HG23 A:THR194 4.8 23.4 1.0 H A:TYR193 4.9 17.5 1.0 CG2 A:ILE197 4.9 25.0 1.0 C A:SER198 5.0 26.5 1.0 C A:PRO195 5.0 24.2 1.0 HG21 A:THR194 5.0 23.4 1.0 H A:GLY199 5.0 32.7 1.0 CA A:ASP200 5.0 18.1 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