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

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

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant, PDB code: 5uud 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 (°)	96.440, 96.440, 105.529, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.3

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

Zinc	(Zn)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf As Cryoprotectant (pdb code 5uud). 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% Dmf As Cryoprotectant, PDB code: 5uud:
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% Dmf 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% Dmf As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:16.9 occ:1.00 O A:GLU187 2.4 16.8 1.0 OD2 A:ASP138 2.4 16.5 1.0 O A:HOH626 2.4 15.1 1.0 OE2 A:GLU190 2.5 17.2 1.0 OE1 A:GLU177 2.5 17.1 1.0 OD1 A:ASP185 2.5 17.9 1.0 OE1 A:GLU190 2.5 17.9 1.0 OE2 A:GLU177 2.7 16.4 1.0 CD A:GLU190 2.8 15.1 1.0 CD A:GLU177 2.9 18.4 1.0 CG A:ASP138 3.4 18.1 1.0 C A:GLU187 3.4 13.4 1.0 CG A:ASP185 3.5 21.7 1.0 HB3 A:ASP138 3.5 18.5 1.0 HA A:ILE188 3.5 20.8 1.0 ZN A:ZN402 3.5 22.0 1.0 OD2 A:ASP185 3.8 19.0 1.0 H A:GLY189 3.8 17.9 1.0 H A:GLU187 3.8 20.5 1.0 CB A:ASP138 3.9 15.4 1.0 HB2 A:GLU187 4.0 23.4 1.0 H A:GLU190 4.1 22.0 1.0 HD13 A:ILE188 4.1 21.0 1.0 O A:ASP185 4.2 16.8 1.0 HB2 A:ASP138 4.2 18.5 1.0 N A:ILE188 4.2 17.2 1.0 CA A:ILE188 4.2 17.4 1.0 N A:GLU187 4.3 17.1 1.0 OD1 A:ASP138 4.3 18.1 1.0 CG A:GLU190 4.3 17.6 1.0 CA A:GLU187 4.3 15.1 1.0 CG A:GLU177 4.4 18.3 1.0 H A:ASP185 4.4 23.0 1.0 N A:GLY189 4.4 14.9 1.0 O A:HOH523 4.5 17.9 1.0 O A:HOH618 4.6 17.4 1.0 HG3 A:GLU190 4.6 21.1 1.0 C A:ASP185 4.6 17.1 1.0 HB2 A:GLU177 4.6 21.1 1.0 CB A:GLU187 4.7 19.5 1.0 CB A:ASP185 4.7 18.4 1.0 C A:ILE188 4.8 15.1 1.0 HB3 A:GLU177 4.8 21.1 1.0 HG2 A:GLU190 4.8 21.1 1.0 HA A:THR174 4.8 19.2 1.0 HG2 A:GLU177 4.8 21.9 1.0 N A:ASP185 4.8 19.2 1.0 HG3 A:GLU177 4.9 21.9 1.0 CB A:GLU177 4.9 17.6 1.0 HB3 A:GLU190 5.0 22.4 1.0 N A:GLU190 5.0 18.4 1.0 OG1 A:THR174 5.0 14.8 1.0 HA A:PRO184 5.0 26.9 1.0

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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% Dmf As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:21.0 occ:1.00 O A:GLN61 2.2 22.0 1.0 O A:HOH790 2.3 20.9 1.0 OD1 A:ASP57 2.3 22.4 1.0 OD1 A:ASP59 2.4 25.7 1.0 O A:HOH622 2.4 25.0 1.0 O A:HOH541 2.4 24.5 1.0 OD2 A:ASP57 2.7 25.0 1.0 CG A:ASP57 2.8 22.0 1.0 H A:GLN61 3.3 26.0 1.0 CG A:ASP59 3.3 28.2 1.0 C A:GLN61 3.4 20.3 1.0 H A:ASP59 3.5 24.5 1.0 HB2 A:GLN61 3.6 30.8 1.0 OD2 A:ASP59 3.7 28.9 1.0 O A:HOH729 4.0 26.9 1.0 N A:GLN61 4.0 21.7 1.0 HA A:PHE62 4.0 25.4 1.0 CA A:GLN61 4.1 21.8 1.0 H A:ALA58 4.2 24.6 1.0 CB A:ASP57 4.3 19.9 1.0 N A:ASP59 4.3 20.4 1.0 CB A:GLN61 4.3 25.7 1.0 H A:ASN60 4.4 29.6 1.0 O A:HOH739 4.4 22.0 1.0 N A:PHE62 4.5 21.4 1.0 O A:HOH868 4.5 34.6 1.0 O A:HOH549 4.6 21.1 1.0 OD2 A:ASP67 4.6 23.6 1.0 CB A:ASP59 4.6 25.2 1.0 O A:HOH866 4.6 30.8 1.0 HB2 A:ASP57 4.7 23.9 1.0 N A:ALA58 4.7 20.5 1.0 N A:ASN60 4.7 24.7 1.0 O A:HOH895 4.7 35.4 1.0 CA A:PHE62 4.7 21.1 1.0 H A:PHE63 4.8 26.0 1.0 HB3 A:ASP57 4.8 23.9 1.0 HB3 A:GLN61 4.8 30.8 1.0 CA A:ASP59 4.8 23.7 1.0 HA A:ASP57 4.8 23.5 1.0 C A:ASP59 4.9 25.4 1.0 HB3 A:ALA58 4.9 27.7 1.0 HB3 A:ASP59 5.0 30.2 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Dmf 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% Dmf As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:24.9 occ:1.00 O A:ILE197 2.3 29.4 1.0 OG1 A:THR194 2.3 23.8 1.0 O A:HOH615 2.3 23.5 1.0 O A:TYR193 2.3 22.4 1.0 O A:THR194 2.3 25.8 1.0 OD1 A:ASP200 2.4 22.6 1.0 O A:HOH785 2.4 28.9 1.0 C A:THR194 3.2 23.0 1.0 C A:TYR193 3.3 19.4 1.0 CB A:THR194 3.4 23.3 1.0 C A:ILE197 3.5 31.6 1.0 CG A:ASP200 3.5 22.6 1.0 HB A:ILE197 3.5 36.2 1.0 H A:ILE197 3.6 33.2 1.0 CA A:THR194 3.6 24.5 1.0 HB A:THR194 3.7 27.9 1.0 OD2 A:ASP200 3.9 26.1 1.0 N A:THR194 3.9 22.1 1.0 H A:ASP200 3.9 27.7 1.0 HA A:SER198 4.0 38.5 1.0 HB3 A:TYR193 4.2 25.7 1.0 CA A:ILE197 4.2 27.8 1.0 HD2 A:TYR193 4.2 29.6 1.0 N A:ILE197 4.3 27.7 1.0 N A:PRO195 4.3 24.8 1.0 HA A:PRO195 4.3 31.9 1.0 CB A:ILE197 4.3 30.2 1.0 O A:HOH638 4.4 50.5 1.0 N A:SER198 4.5 30.1 1.0 O A:HOH809 4.5 57.7 1.0 O A:ASP200 4.5 21.3 1.0 O A:GLU190 4.5 20.2 1.0 CA A:TYR193 4.6 20.8 1.0 O A:HOH803 4.6 34.4 1.0 HA A:THR194 4.6 29.4 1.0 CA A:SER198 4.6 32.1 1.0 HG22 A:ILE197 4.6 36.5 1.0 CG2 A:THR194 4.6 23.7 1.0 CA A:PRO195 4.7 26.6 1.0 N A:ASP200 4.7 23.1 1.0 H A:THR194 4.7 26.6 1.0 CB A:TYR193 4.7 21.4 1.0 HG23 A:THR194 4.8 28.4 1.0 CB A:ASP200 4.8 22.0 1.0 CD2 A:TYR193 4.8 24.6 1.0 C A:ASP200 4.8 19.1 1.0 O A:HOH629 4.9 35.5 1.0 H A:GLY199 4.9 36.2 1.0 HG21 A:THR194 4.9 28.4 1.0 H A:TYR193 4.9 24.1 1.0 C A:SER198 4.9 29.6 1.0 C A:PRO195 5.0 28.0 1.0 CA A:ASP200 5.0 23.1 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