Calcium in PDB 5un3: Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose

All present enzymatic activity of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose:
3.4.24.27;

The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose, PDB code: 5un3 was solved by D.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.21 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.659, 97.659, 108.069, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.1

The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose (pdb code 5un3). 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 (295 K) in the Presence of 50% Xylose, PDB code: 5un3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca317 b:14.7 occ:1.00 OD2 A:ASP138 2.3 14.6 1.0 O A:GLU187 2.4 14.4 1.0 O A:HOH487 2.4 15.7 1.0 OE1 A:GLU177 2.5 14.7 1.0 OD1 A:ASP185 2.5 16.1 1.0 OE1 A:GLU190 2.5 15.1 1.0 OE2 A:GLU190 2.5 15.7 1.0 OE2 A:GLU177 2.8 16.4 1.0 CD A:GLU190 2.8 13.3 1.0 CD A:GLU177 3.0 15.8 1.0 CG A:ASP138 3.4 16.2 1.0 C A:GLU187 3.4 13.5 1.0 CG A:ASP185 3.5 16.9 1.0 HB3 A:ASP138 3.5 18.1 1.0 HA A:ILE188 3.6 17.6 1.0 ZN A:ZN318 3.6 18.1 1.0 H A:GLY189 3.7 17.0 1.0 H A:GLU187 3.8 19.9 1.0 OD2 A:ASP185 3.9 15.9 1.0 CB A:ASP138 4.0 15.1 1.0 HB2 A:GLU187 4.0 22.1 1.0 H A:GLU190 4.1 20.9 1.0 HD13 A:ILE188 4.2 23.1 1.0 HB2 A:ASP138 4.2 18.1 1.0 N A:ILE188 4.2 14.1 1.0 O A:HOH463 4.2 41.6 1.0 O A:ASP185 4.2 15.1 1.0 OD1 A:ASP138 4.3 16.9 1.0 N A:GLU187 4.3 16.6 1.0 CA A:ILE188 4.3 14.6 1.0 H A:ASP185 4.3 18.1 1.0 CA A:GLU187 4.3 14.9 1.0 CG A:GLU190 4.3 13.9 1.0 N A:GLY189 4.4 14.1 1.0 CG A:GLU177 4.4 15.7 1.0 O A:HOH452 4.4 18.3 1.0 O A:HOH427 4.6 14.7 1.0 HG3 A:GLU190 4.6 16.6 1.0 C A:ASP185 4.7 16.0 1.0 HB2 A:GLU177 4.7 20.4 1.0 CB A:GLU187 4.7 18.4 1.0 C A:ILE188 4.8 15.0 1.0 CB A:ASP185 4.8 16.7 1.0 HB3 A:GLU177 4.8 20.4 1.0 HA A:THR174 4.8 16.7 1.0 HG2 A:GLU190 4.8 16.6 1.0 N A:ASP185 4.8 15.1 1.0 HG2 A:GLU177 4.8 18.8 1.0 CB A:GLU177 4.9 17.0 1.0 HB3 A:GLU190 4.9 19.9 1.0 HG3 A:GLU177 4.9 18.8 1.0 OG1 A:THR174 4.9 15.8 1.0 N A:GLU190 4.9 17.4 1.0

Calcium binding site 2 out of 3 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:19.2 occ:1.00 O A:GLN61 2.2 22.3 1.0 O A:HOH586 2.2 24.6 1.0 OD1 A:ASP59 2.2 26.4 1.0 OD1 A:ASP57 2.3 22.5 1.0 O A:HOH410 2.4 29.4 1.0 O A:HOH451 2.4 23.4 1.0 OD2 A:ASP57 2.7 26.1 1.0 CG A:ASP57 2.8 20.8 1.0 H A:GLN61 3.2 25.3 1.0 CG A:ASP59 3.2 27.5 1.0 C A:GLN61 3.4 23.4 1.0 H A:ASP59 3.5 27.5 1.0 OD2 A:ASP59 3.6 29.7 1.0 HB2 A:GLN61 3.7 35.6 1.0 N A:GLN61 3.9 21.1 1.0 HA A:PHE62 3.9 26.1 1.0 O A:HOH553 4.0 38.1 1.0 H A:ALA58 4.1 24.3 1.0 CA A:GLN61 4.1 23.6 1.0 N A:ASP59 4.2 22.9 1.0 CB A:ASP57 4.3 20.8 1.0 CB A:GLN61 4.3 29.6 1.0 H A:ASN60 4.4 28.6 1.0 N A:PHE62 4.4 21.8 1.0 CB A:ASP59 4.5 25.5 1.0 O A:HOH444 4.5 19.1 1.0 O A:HOH632 4.6 37.7 1.0 OD2 A:ASP67 4.6 19.7 1.0 N A:ALA58 4.6 20.3 1.0 HB2 A:ASP57 4.6 24.9 1.0 CA A:PHE62 4.7 21.7 1.0 N A:ASN60 4.7 23.8 1.0 H A:PHE63 4.7 29.0 1.0 CA A:ASP59 4.7 24.4 1.0 HB3 A:ASP57 4.8 24.9 1.0 HA A:ASP57 4.8 23.8 1.0 HB3 A:GLN61 4.8 35.6 1.0 C A:ASP59 4.8 25.9 1.0 HB3 A:ALA58 4.9 31.9 1.0 HB3 A:ASP59 4.9 30.6 1.0

Calcium binding site 3 out of 3 in the Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetragonal Thermolysin (295 K) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca320 b:22.9 occ:1.00 O A:ILE197 2.3 31.1 1.0 O A:TYR193 2.3 20.3 1.0 OG1 A:THR194 2.4 22.7 1.0 O A:HOH456 2.4 20.8 1.0 OD1 A:ASP200 2.4 23.0 1.0 O A:THR194 2.4 26.7 1.0 O A:HOH595 2.4 27.7 1.0 C A:THR194 3.2 23.8 1.0 C A:TYR193 3.4 21.7 1.0 HB A:ILE197 3.4 42.9 1.0 CG A:ASP200 3.4 22.6 1.0 C A:ILE197 3.5 33.8 1.0 CB A:THR194 3.5 24.7 1.0 H A:ILE197 3.5 47.9 1.0 CA A:THR194 3.7 25.5 1.0 OD2 A:ASP200 3.8 24.4 1.0 HB A:THR194 3.8 29.6 1.0 H A:ASP200 3.9 28.4 1.0 N A:THR194 3.9 25.0 1.0 CA A:ILE197 4.1 34.7 1.0 CB A:ILE197 4.2 35.8 1.0 N A:ILE197 4.2 39.9 1.0 HB3 A:TYR193 4.2 24.1 1.0 HD2 A:TYR193 4.2 31.5 1.0 HA A:SER198 4.2 41.9 1.0 HA A:PRO195 4.3 32.7 1.0 N A:PRO195 4.3 23.7 1.0 HG22 A:ILE197 4.3 44.9 1.0 N A:SER198 4.5 32.5 1.0 O A:GLU190 4.5 19.7 1.0 O A:ASP200 4.5 21.4 1.0 CA A:TYR193 4.6 20.6 1.0 O A:HOH538 4.6 52.5 1.0 HA A:THR194 4.6 30.6 1.0 O A:HOH589 4.6 41.7 1.0 N A:ASP200 4.7 23.7 1.0 CA A:PRO195 4.7 27.2 1.0 H A:THR194 4.7 30.0 1.0 CG2 A:THR194 4.7 26.5 1.0 O A:HOH547 4.7 56.0 1.0 CB A:ASP200 4.8 21.5 1.0 CD2 A:TYR193 4.8 26.2 1.0 CA A:SER198 4.8 35.0 1.0 H A:GLY199 4.8 35.1 1.0 CB A:TYR193 4.8 20.1 1.0 HG23 A:THR194 4.8 31.8 1.0 CG2 A:ILE197 4.8 37.4 1.0 C A:ASP200 4.8 20.1 1.0 H A:TYR193 4.9 21.4 1.0 C A:PRO195 4.9 30.0 1.0 HG21 A:THR194 5.0 31.8 1.0 CA A:ASP200 5.0 22.4 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