Calcium in PDB 6n4z: Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K

All present enzymatic activity of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K:
3.4.24.27;

The structure of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K, PDB code: 6n4z was solved by D.H.Juers, K.Harrison, B.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.40 / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.725, 96.725, 106.535, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 16.1

The structure of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K (pdb code 6n4z). 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 (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K, PDB code: 6n4z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.1 occ:1.00 O A:GLN61 2.3 19.5 1.0 O A:HOH819 2.3 17.9 1.0 OD1 A:ASP59 2.3 19.2 1.0 OD1 A:ASP57 2.4 18.7 1.0 O A:HOH560 2.4 20.6 1.0 O A:HOH621 2.4 19.3 1.0 OD2 A:ASP57 2.6 19.1 1.0 CG A:ASP57 2.8 17.1 1.0 H A:GLN61 3.2 22.5 0.4 H A:GLN61 3.2 22.5 0.6 CG A:ASP59 3.3 20.6 1.0 C A:GLN61 3.4 19.0 1.0 H A:ASP59 3.5 23.0 1.0 HB2 A:GLN61 3.5 25.9 0.4 HB2 A:GLN61 3.6 26.0 0.6 OD2 A:ASP59 3.8 23.3 1.0 N A:GLN61 3.9 18.8 1.0 O A:HOH755 4.0 23.6 1.0 HA A:PHE62 4.0 21.1 1.0 CA A:GLN61 4.1 19.3 0.6 CA A:GLN61 4.1 19.5 0.4 H A:ALA58 4.2 21.2 1.0 N A:ASP59 4.3 19.1 1.0 CB A:GLN61 4.3 21.7 0.6 CB A:GLN61 4.3 21.6 0.4 CB A:ASP57 4.3 16.1 1.0 H A:ASN60 4.4 22.2 1.0 O A:HOH890 4.4 19.9 0.5 N A:PHE62 4.5 18.4 1.0 O A:HOH890 4.5 19.4 0.6 CB A:ASP59 4.6 19.8 1.0 O A:HOH882 4.6 25.0 1.0 OD2 A:ASP67 4.6 17.6 1.0 O A:HOH550 4.6 16.8 1.0 N A:ASN60 4.6 18.5 1.0 N A:ALA58 4.7 17.7 1.0 HB2 A:ASP57 4.7 19.3 1.0 O A:HOH912 4.7 37.9 1.0 HB3 A:GLN61 4.7 26.0 0.6 CA A:ASP59 4.7 18.8 1.0 CA A:PHE62 4.8 17.6 1.0 HB3 A:ASP57 4.8 19.3 1.0 HA A:ASP57 4.8 19.2 1.0 H A:PHE63 4.8 23.1 1.0 C A:ASP59 4.8 18.9 1.0 HB3 A:ALA58 4.9 24.1 1.0 HB3 A:ASP59 4.9 23.7 1.0 HB3 A:GLN61 4.9 25.9 0.4 HG2 A:GLN61 5.0 29.1 0.4

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:13.9 occ:1.00 O A:GLU187 2.4 14.6 1.0 OD2 A:ASP138 2.4 13.8 1.0 OE1 A:GLU177 2.4 14.5 1.0 O A:HOH641 2.4 12.4 1.0 OD1 A:ASP185 2.4 14.8 1.0 OE1 A:GLU190 2.5 14.0 1.0 OE2 A:GLU190 2.5 15.2 1.0 OE2 A:GLU177 2.7 14.5 1.0 CD A:GLU190 2.8 14.6 1.0 CD A:GLU177 2.9 14.7 1.0 CG A:ASP138 3.3 13.8 1.0 C A:GLU187 3.4 14.6 1.0 CG A:ASP185 3.5 15.3 1.0 HB3 A:ASP138 3.5 14.8 1.0 HA A:ILE188 3.5 16.9 1.0 ZN A:ZN407 3.5 16.3 0.9 H A:GLY189 3.8 17.3 1.0 H A:GLU187 3.8 18.6 0.6 H A:GLU187 3.8 18.6 0.4 OD2 A:ASP185 3.8 15.3 1.0 HB2 A:GLU187 3.9 20.7 0.6 CB A:ASP138 3.9 12.3 1.0 H A:GLU190 4.1 17.7 1.0 O A:ASP185 4.2 14.0 1.0 HB2 A:GLU187 4.2 20.9 0.4 HB2 A:ASP138 4.2 14.8 1.0 OD1 A:ASP138 4.2 15.1 1.0 HD13 A:ILE188 4.2 18.3 1.0 N A:ILE188 4.2 15.0 1.0 N A:GLU187 4.3 15.5 1.0 CA A:ILE188 4.3 14.1 1.0 CG A:GLU190 4.3 15.3 1.0 H A:ASP185 4.3 17.8 1.0 CA A:GLU187 4.3 15.8 0.6 CG A:GLU177 4.4 14.9 1.0 CA A:GLU187 4.4 15.8 0.4 N A:GLY189 4.4 14.4 1.0 O A:HOH522 4.5 15.0 1.0 O A:HOH605 4.5 16.5 1.0 HG3 A:GLU190 4.6 18.4 1.0 C A:ASP185 4.6 14.7 1.0 CB A:GLU187 4.6 17.3 0.6 HB2 A:GLU177 4.7 17.2 1.0 CB A:ASP185 4.7 15.0 1.0 HB3 A:GLU177 4.7 17.2 1.0 HG2 A:GLU190 4.7 18.4 1.0 C A:ILE188 4.8 14.4 1.0 HG2 A:GLU177 4.8 17.9 1.0 N A:ASP185 4.8 14.8 1.0 CB A:GLU187 4.8 17.4 0.4 HA A:THR174 4.8 14.9 1.0 HG3 A:GLU177 4.8 17.9 1.0 CB A:GLU177 4.9 14.3 1.0 HB3 A:GLU190 4.9 18.2 1.0 N A:GLU190 4.9 14.8 1.0 HA A:PRO184 5.0 19.4 1.0 HB2 A:ASP185 5.0 18.0 1.0 CA A:ASP185 5.0 14.7 1.0 OG1 A:THR174 5.0 12.9 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetragonal Thermolysin (with 50% Xylose) Plunge Cooled in Liquid Nitrogen to 77 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:22.2 occ:1.00 O A:ILE197 2.3 28.4 1.0 OD2 A:ASP200 2.4 23.7 1.0 OG1 A:THR194 2.4 24.7 1.0 O A:TYR193 2.4 19.4 1.0 O A:HOH566 2.4 19.1 1.0 O A:THR194 2.4 23.4 1.0 O A:HOH802 2.5 24.8 1.0 C A:THR194 3.2 23.0 1.0 C A:TYR193 3.4 18.8 1.0 HB A:ILE197 3.4 37.4 1.0 CG A:ASP200 3.4 25.4 1.0 CB A:THR194 3.4 24.1 1.0 C A:ILE197 3.5 29.5 1.0 H A:ILE197 3.6 36.9 1.0 CA A:THR194 3.7 22.3 1.0 HB A:THR194 3.7 28.9 1.0 OD1 A:ASP200 3.8 26.8 1.0 H A:ASP200 3.9 30.8 1.0 N A:THR194 3.9 20.7 1.0 HA A:SER198 4.1 37.4 0.6 HA A:SER198 4.1 37.4 0.4 HB3 A:TYR193 4.2 23.7 1.0 CA A:ILE197 4.2 30.2 1.0 CB A:ILE197 4.2 31.2 1.0 N A:ILE197 4.3 30.7 1.0 N A:PRO195 4.3 24.5 1.0 HD2 A:TYR193 4.3 26.9 1.0 HA A:PRO195 4.3 31.3 1.0 HG22 A:ILE197 4.3 37.8 1.0 O A:HOH796 4.4 40.8 0.9 O A:ASP200 4.5 22.0 1.0 N A:SER198 4.5 30.7 1.0 O A:GLU190 4.5 17.4 1.0 CA A:TYR193 4.6 17.9 1.0 HA A:THR194 4.6 26.8 1.0 O A:HOH792 4.7 26.5 0.8 CA A:PRO195 4.7 26.1 1.0 N A:ASP200 4.7 25.6 1.0 CA A:SER198 4.7 31.2 0.6 CA A:SER198 4.7 31.2 0.4 CG2 A:THR194 4.7 24.2 1.0 CB A:ASP200 4.8 24.3 1.0 CB A:TYR193 4.8 19.8 1.0 H A:THR194 4.8 24.8 1.0 CD2 A:TYR193 4.8 22.4 1.0 CG2 A:ILE197 4.8 31.5 1.0 C A:ASP200 4.8 21.5 1.0 H A:GLY199 4.8 35.8 1.0 O A:HOH808 4.9 44.8 0.9 HG23 A:THR194 4.9 29.1 1.0 C A:PRO195 5.0 29.3 1.0 H A:TYR193 5.0 20.3 1.0 C A:SER198 5.0 30.8 1.0 HG21 A:THR194 5.0 29.1 1.0 CA A:ASP200 5.0 24.1 1.0

K.Harrison, Z.Wu, D.H.Juers. A Comparison of Gas Stream Cooling and Plunge Cooling of Macromolecular Crystals. J.Appl.Crystallogr. V. 52 1222 2019.
ISSN: ISSN 0021-8898
PubMed: 31636524
DOI: 10.1107/S1600576719010318