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

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

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol As Cryoprotectant, PDB code: 5uue 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)	20.80 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.149, 96.149, 104.800, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.5

The structure of Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant (pdb code 5uue). 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% Methanol As Cryoprotectant, PDB code: 5uue:
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% Methanol 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% Methanol As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:16.6 occ:1.00 O A:GLU187 2.3 14.8 1.0 OD2 A:ASP138 2.4 15.4 1.0 OE1 A:GLU177 2.4 15.0 1.0 OE2 A:GLU190 2.5 14.7 1.0 OD1 A:ASP185 2.5 18.4 1.0 O A:HOH587 2.5 13.2 1.0 OE1 A:GLU190 2.5 14.3 1.0 OE2 A:GLU177 2.8 16.9 1.0 CD A:GLU190 2.8 13.9 1.0 CD A:GLU177 2.9 16.9 1.0 C A:GLU187 3.3 15.2 1.0 CG A:ASP138 3.4 15.5 1.0 CG A:ASP185 3.5 23.9 1.0 HB3 A:ASP138 3.5 17.0 1.0 HA A:ILE188 3.5 17.4 1.0 ZN A:ZN402 3.6 21.8 1.0 H A:GLU187 3.8 20.2 0.4 OD2 A:ASP185 3.8 18.0 1.0 H A:GLU187 3.8 20.2 0.6 H A:GLY189 3.8 16.0 1.0 HB2 A:GLU187 3.9 26.9 0.6 CB A:ASP138 3.9 14.2 1.0 HD13 A:ILE188 4.0 19.6 1.0 O A:ASP185 4.1 15.9 1.0 O A:HOH527 4.1 35.4 1.0 N A:ILE188 4.1 16.2 1.0 HB2 A:GLU187 4.2 25.8 0.4 H A:GLU190 4.2 23.8 1.0 N A:GLU187 4.2 16.8 1.0 CA A:ILE188 4.2 14.5 1.0 HB2 A:ASP138 4.2 17.0 1.0 CA A:GLU187 4.3 18.9 0.6 OD1 A:ASP138 4.3 16.1 1.0 CA A:GLU187 4.3 18.3 0.4 H A:ASP185 4.3 23.1 1.0 CG A:GLU190 4.3 18.4 1.0 CG A:GLU177 4.4 17.3 1.0 N A:GLY189 4.4 13.3 1.0 O A:HOH598 4.5 20.9 1.0 C A:ASP185 4.6 13.7 1.0 CB A:GLU187 4.6 22.4 0.6 O A:HOH562 4.6 19.1 1.0 HG3 A:GLU190 4.6 22.0 1.0 HB2 A:GLU177 4.6 18.9 1.0 CB A:GLU187 4.7 21.5 0.4 HA A:THR174 4.8 19.8 1.0 CB A:ASP185 4.8 20.9 1.0 C A:ILE188 4.8 15.1 1.0 HG2 A:GLU190 4.8 22.0 1.0 HB3 A:GLU177 4.8 18.9 1.0 N A:ASP185 4.8 19.2 1.0 HG2 A:GLU177 4.9 20.8 1.0 HG3 A:GLU177 4.9 20.8 1.0 OG1 A:THR174 4.9 13.6 1.0 HB3 A:GLU190 4.9 22.2 1.0 CB A:GLU177 4.9 15.8 1.0 H A:ILE188 4.9 19.4 1.0 N A:GLU190 5.0 19.8 1.0 HB3 A:GLU187 5.0 26.9 0.6

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:27.4 occ:1.00 OD1 A:ASP57 2.2 36.8 1.0 O A:GLN61 2.2 29.4 1.0 OD1 A:ASP59 2.3 31.7 1.0 O A:HOH730 2.3 26.5 1.0 O A:HOH618 2.4 26.0 1.0 OD2 A:ASP57 2.4 36.4 1.0 O A:HOH542 2.4 32.9 1.0 CG A:ASP57 2.6 35.1 1.0 CG A:ASP59 3.2 34.5 1.0 H A:GLN61 3.3 30.3 1.0 H A:ASP59 3.3 29.7 1.0 C A:GLN61 3.4 29.6 1.0 OD2 A:ASP59 3.6 32.2 1.0 HB2 A:GLN61 3.6 44.5 1.0 N A:GLN61 3.9 25.3 1.0 HA A:PHE62 4.0 30.6 1.0 O A:HOH681 4.0 32.4 1.0 H A:ALA58 4.1 32.4 1.0 CA A:GLN61 4.1 31.4 1.0 N A:ASP59 4.1 24.7 1.0 CB A:ASP57 4.1 29.4 1.0 H A:ASN60 4.3 37.7 1.0 O A:HOH863 4.3 50.8 1.0 CB A:GLN61 4.3 37.1 1.0 N A:PHE62 4.5 26.2 1.0 CB A:ASP59 4.5 29.8 1.0 HB2 A:ASP57 4.5 35.3 1.0 N A:ALA58 4.6 27.0 1.0 HB3 A:ASP57 4.6 35.3 1.0 N A:ASN60 4.6 31.4 1.0 O A:HOH849 4.6 35.1 1.0 OD2 A:ASP67 4.6 25.8 1.0 CA A:ASP59 4.7 28.7 1.0 CA A:PHE62 4.7 25.5 1.0 O A:HOH513 4.7 30.6 1.0 C A:ASP59 4.8 32.0 1.0 HB3 A:ALA58 4.8 32.4 1.0 H A:PHE63 4.8 30.4 1.0 HA A:ASP57 4.8 32.7 1.0 HB3 A:GLN61 4.8 44.5 1.0 HB3 A:ASP59 4.9 35.7 1.0 CA A:ASP57 4.9 27.2 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin Cryocooled to 100 K with 50% Methanol 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% Methanol As Cryoprotectant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:24.1 occ:1.00 O A:ILE197 2.3 30.1 1.0 OD1 A:ASP200 2.3 21.3 1.0 OG1 A:THR194 2.4 20.6 1.0 O A:TYR193 2.4 22.4 1.0 O A:HOH577 2.4 22.1 1.0 O A:THR194 2.4 25.6 1.0 O A:HOH782 2.4 30.0 1.0 C A:THR194 3.2 24.6 1.0 C A:TYR193 3.4 20.4 1.0 CG A:ASP200 3.4 21.6 1.0 CB A:THR194 3.5 23.9 1.0 C A:ILE197 3.5 32.5 1.0 HB A:ILE197 3.6 33.6 1.0 CA A:THR194 3.7 23.4 1.0 H A:ILE197 3.8 38.7 1.0 OD2 A:ASP200 3.8 23.9 1.0 HB A:THR194 3.8 28.7 1.0 HA A:SER198 3.8 37.2 1.0 H A:ASP200 3.9 31.8 1.0 N A:THR194 3.9 22.1 1.0 HD2 A:TYR193 4.1 28.9 1.0 HB3 A:TYR193 4.2 20.8 1.0 HA A:PRO195 4.2 32.6 1.0 N A:PRO195 4.3 24.5 1.0 CA A:ILE197 4.3 28.1 1.0 O A:HOH691 4.4 42.4 1.0 N A:ILE197 4.4 32.3 1.0 CB A:ILE197 4.4 28.0 1.0 N A:SER198 4.5 30.8 1.0 O A:ASP200 4.5 20.2 1.0 CA A:SER198 4.5 31.0 1.0 HG22 A:ILE197 4.5 33.0 1.0 CA A:TYR193 4.6 20.6 1.0 O A:GLU190 4.6 20.4 1.0 HA A:THR194 4.6 28.1 1.0 N A:ASP200 4.7 26.5 1.0 CA A:PRO195 4.7 27.2 1.0 CD2 A:TYR193 4.7 24.1 1.0 CG2 A:THR194 4.7 21.1 1.0 CB A:ASP200 4.7 24.7 1.0 H A:THR194 4.8 26.5 1.0 CB A:TYR193 4.8 17.3 1.0 C A:ASP200 4.8 19.7 1.0 HG23 A:THR194 4.8 25.3 1.0 H A:GLY199 4.8 32.3 1.0 C A:SER198 4.9 28.2 1.0 O A:HOH790 4.9 34.4 1.0 H A:TYR193 4.9 23.7 1.0 HG21 A:THR194 5.0 25.3 1.0 CA A:ASP200 5.0 23.4 1.0 CG2 A:ILE197 5.0 27.5 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