Calcium in PDB 5uub: Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant

All present enzymatic activity of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant:
3.4.24.27;

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant, PDB code: 5uub 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)	20.90 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.707, 96.707, 105.611, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.5

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant also contains other interesting chemical elements:

Zinc	(Zn)	7 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% Mpd As Cryoprotectant (pdb code 5uub). 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 25% Xylose/25% Mpd As Cryoprotectant, PDB code: 5uub:
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 25% Xylose/25% 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 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:13.0 occ:1.00 O A:GLU187 2.3 13.1 1.0 OD2 A:ASP138 2.4 13.1 1.0 O A:HOH580 2.4 12.6 1.0 OE1 A:GLU177 2.4 13.2 1.0 OD1 A:ASP185 2.5 13.6 1.0 OE2 A:GLU190 2.5 13.2 1.0 OE1 A:GLU190 2.5 13.5 1.0 OE2 A:GLU177 2.7 12.8 1.0 CD A:GLU190 2.8 11.4 1.0 CD A:GLU177 2.9 12.5 1.0 CG A:ASP138 3.4 13.8 1.0 C A:GLU187 3.4 12.8 1.0 CG A:ASP185 3.4 15.2 1.0 HA A:ILE188 3.5 14.8 1.0 HB3 A:ASP138 3.5 14.0 1.0 ZN A:ZN402 3.6 16.3 1.0 H A:GLY189 3.8 15.0 1.0 OD2 A:ASP185 3.8 14.2 1.0 H A:GLU187 3.8 16.4 0.6 H A:GLU187 3.8 16.4 0.4 HB2 A:GLU187 3.9 16.6 0.4 CB A:ASP138 4.0 11.7 1.0 O A:ASP185 4.1 14.9 1.0 HD13 A:ILE188 4.2 17.8 1.0 H A:GLU190 4.2 17.0 1.0 N A:ILE188 4.2 13.9 1.0 HB2 A:ASP138 4.2 14.0 1.0 CA A:ILE188 4.3 12.3 1.0 O A:HOH631 4.3 34.4 1.0 N A:GLU187 4.3 13.7 1.0 H A:ASP185 4.3 15.6 1.0 OD1 A:ASP138 4.3 14.5 1.0 CA A:GLU187 4.3 12.4 0.4 CG A:GLU190 4.3 12.3 1.0 CA A:GLU187 4.4 13.2 0.6 CG A:GLU177 4.4 13.7 1.0 HB2 A:GLU187 4.4 20.1 0.6 N A:GLY189 4.4 12.5 1.0 O A:HOH535 4.5 13.7 1.0 O A:HOH600 4.5 15.1 1.0 HG3 A:GLU190 4.6 14.7 1.0 C A:ASP185 4.6 14.0 1.0 CB A:GLU187 4.6 13.8 0.4 HB2 A:GLU177 4.6 16.7 1.0 CB A:ASP185 4.7 13.5 1.0 HG2 A:GLU190 4.8 14.7 1.0 C A:ILE188 4.8 12.3 1.0 HB3 A:GLU177 4.8 16.7 1.0 N A:ASP185 4.8 13.0 1.0 HA A:THR174 4.8 16.0 1.0 HG2 A:GLU177 4.8 16.4 1.0 HG3 A:GLU177 4.9 16.4 1.0 CB A:GLU177 4.9 13.9 1.0 HB2 A:ASP185 4.9 16.2 1.0 HB3 A:GLU190 4.9 16.0 1.0 CB A:GLU187 4.9 16.7 0.6 OG1 A:THR174 5.0 12.0 1.0 N A:GLU190 5.0 14.2 1.0 CA A:ASP185 5.0 12.7 1.0 H A:ILE188 5.0 16.6 1.0

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% 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 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.1 occ:1.00 O A:GLN61 2.2 18.5 1.0 OD1 A:ASP57 2.3 16.3 1.0 O A:HOH787 2.3 17.9 1.0 OD1 A:ASP59 2.3 19.9 1.0 O A:HOH650 2.4 18.2 1.0 O A:HOH548 2.4 21.4 1.0 OD2 A:ASP57 2.7 21.0 1.0 CG A:ASP57 2.8 17.8 1.0 H A:GLN61 3.3 20.8 1.0 CG A:ASP59 3.3 21.1 1.0 C A:GLN61 3.4 18.1 1.0 H A:ASP59 3.5 22.0 1.0 HB2 A:GLN61 3.6 27.4 1.0 OD2 A:ASP59 3.7 24.2 1.0 O A:HOH745 3.9 22.4 1.0 N A:GLN61 4.0 17.3 1.0 HA A:PHE62 4.1 21.3 1.0 CA A:GLN61 4.1 18.7 1.0 H A:ALA58 4.1 19.3 1.0 N A:ASP59 4.3 18.3 1.0 CB A:ASP57 4.3 15.2 1.0 CB A:GLN61 4.4 22.8 1.0 H A:ASN60 4.4 22.8 1.0 N A:PHE62 4.5 17.8 1.0 O A:HOH571 4.5 14.9 1.0 CB A:ASP59 4.6 20.7 1.0 OD2 A:ASP67 4.6 15.8 1.0 N A:ALA58 4.6 16.1 1.0 HB2 A:ASP57 4.6 18.3 1.0 O A:HOH828 4.7 24.7 1.0 O A:HOH851 4.7 42.3 1.0 N A:ASN60 4.7 19.0 1.0 CA A:PHE62 4.8 17.8 1.0 CA A:ASP59 4.8 20.6 1.0 HB3 A:ASP57 4.8 18.3 1.0 HA A:ASP57 4.8 16.5 1.0 H A:PHE63 4.8 21.2 1.0 HB3 A:GLN61 4.8 27.4 1.0 HB3 A:ALA58 4.8 22.5 1.0 C A:ASP59 4.9 21.5 1.0 HB3 A:ASP59 4.9 24.8 1.0 CA A:ASP57 5.0 13.7 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 25% Xylose/25% 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 25% Xylose/25% Mpd As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:21.5 occ:1.00 O A:ILE197 2.3 25.4 1.0 OD1 A:ASP200 2.3 19.6 1.0 OG1 A:THR194 2.4 19.0 1.0 O A:TYR193 2.4 17.1 1.0 O A:THR194 2.4 20.5 1.0 O A:HOH573 2.4 17.3 1.0 O A:HOH757 2.4 24.2 1.0 C A:THR194 3.2 20.6 1.0 C A:TYR193 3.4 16.8 1.0 CG A:ASP200 3.4 18.5 1.0 CB A:THR194 3.4 19.2 1.0 HB A:ILE197 3.4 29.3 1.0 C A:ILE197 3.5 27.9 1.0 H A:ILE197 3.6 33.1 1.0 CA A:THR194 3.7 19.8 1.0 HB A:THR194 3.7 23.1 1.0 OD2 A:ASP200 3.8 21.5 1.0 N A:THR194 3.9 18.5 1.0 H A:ASP200 3.9 26.2 1.0 HA A:SER198 4.1 32.6 1.0 CA A:ILE197 4.2 24.8 1.0 HB3 A:TYR193 4.2 21.6 1.0 CB A:ILE197 4.2 24.4 1.0 HD2 A:TYR193 4.2 24.1 1.0 HA A:PRO195 4.2 27.3 1.0 N A:PRO195 4.3 19.8 1.0 N A:ILE197 4.3 27.6 1.0 O A:HOH629 4.3 40.6 1.0 HG22 A:ILE197 4.4 33.3 1.0 O A:ASP200 4.5 18.8 1.0 N A:SER198 4.5 25.6 1.0 O A:HOH682 4.6 41.3 1.0 CA A:TYR193 4.6 15.5 1.0 O A:GLU190 4.6 16.9 1.0 HA A:THR194 4.6 23.7 1.0 O A:HOH793 4.6 32.9 1.0 CA A:PRO195 4.6 22.8 1.0 CA A:SER198 4.7 27.2 1.0 N A:ASP200 4.7 21.8 1.0 H A:THR194 4.7 22.2 1.0 CG2 A:THR194 4.7 20.4 1.0 CB A:ASP200 4.7 19.2 1.0 CD2 A:TYR193 4.7 20.1 1.0 CB A:TYR193 4.8 18.0 1.0 C A:ASP200 4.8 17.0 1.0 CG2 A:ILE197 4.9 27.8 1.0 HG23 A:THR194 4.9 24.5 1.0 H A:TYR193 4.9 18.4 1.0 C A:PRO195 5.0 23.7 1.0 HG21 A:THR194 5.0 24.5 1.0 H A:GLY199 5.0 31.3 1.0 CA A:ASP200 5.0 18.5 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