Calcium in PDB 5uu7: Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd

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

The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd, PDB code: 5uu7 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)	20.76 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.026, 98.026, 107.522, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 15.6

The structure of Tetragonal Thermolysin (295 K) in the Presence of 50% Mpd 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% Mpd (pdb code 5uu7). 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% Mpd, PDB code: 5uu7:
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% Mpd


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% Mpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.4 occ:1.00 O A:GLU187 2.3 14.3 1.0 OD2 A:ASP138 2.4 14.0 1.0 O A:HOH584 2.4 14.2 1.0 OE1 A:GLU177 2.5 15.2 1.0 OD1 A:ASP185 2.5 14.9 1.0 OE1 A:GLU190 2.5 16.1 1.0 OE2 A:GLU190 2.5 14.2 1.0 OE2 A:GLU177 2.8 15.4 1.0 CD A:GLU190 2.8 13.2 1.0 CD A:GLU177 3.0 15.9 1.0 CG A:ASP138 3.4 16.8 1.0 C A:GLU187 3.4 13.3 1.0 CG A:ASP185 3.5 17.4 1.0 HB3 A:ASP138 3.5 16.4 1.0 ZN A:ZN402 3.6 16.1 0.9 HA A:ILE188 3.6 16.7 1.0 H A:GLU187 3.8 19.3 1.0 H A:GLY189 3.8 16.7 1.0 OD2 A:ASP185 3.8 15.8 1.0 CB A:ASP138 4.0 13.7 1.0 HB2 A:GLU187 4.0 22.2 1.0 H A:GLU190 4.2 20.5 1.0 O A:HOH561 4.2 31.1 1.0 O A:ASP185 4.2 15.9 1.0 HD13 A:ILE188 4.2 22.4 1.0 N A:ILE188 4.2 13.8 1.0 HB2 A:ASP138 4.2 16.4 1.0 N A:GLU187 4.3 16.1 1.0 OD1 A:ASP138 4.3 16.9 1.0 CA A:ILE188 4.3 13.9 1.0 H A:ASP185 4.3 17.7 1.0 CG A:GLU190 4.3 14.8 1.0 CA A:GLU187 4.3 15.2 1.0 CG A:GLU177 4.4 14.7 1.0 N A:GLY189 4.4 13.9 1.0 O A:HOH562 4.5 20.4 1.0 O A:HOH525 4.6 15.6 1.0 HG3 A:GLU190 4.6 17.8 1.0 C A:ASP185 4.7 16.1 1.0 CB A:GLU187 4.7 18.5 1.0 HB2 A:GLU177 4.7 18.6 1.0 CB A:ASP185 4.8 16.2 1.0 C A:ILE188 4.8 14.6 1.0 HA A:THR174 4.8 16.5 1.0 HG2 A:GLU190 4.8 17.8 1.0 HB3 A:GLU177 4.8 18.6 1.0 N A:ASP185 4.8 14.7 1.0 HG2 A:GLU177 4.8 17.6 1.0 HG3 A:GLU177 4.9 17.6 1.0 HB3 A:GLU190 4.9 18.9 1.0 CB A:GLU177 4.9 15.5 1.0 N A:GLU190 5.0 17.1 1.0 OG1 A:THR174 5.0 16.2 1.0

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


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% Mpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:21.4 occ:1.00 O A:GLN61 2.2 23.1 1.0 OD1 A:ASP59 2.3 24.1 1.0 O A:HOH718 2.3 22.9 1.0 OD1 A:ASP57 2.4 21.5 1.0 O A:HOH522 2.4 27.0 1.0 O A:HOH563 2.5 23.1 1.0 OD2 A:ASP57 2.6 23.9 1.0 CG A:ASP57 2.8 21.1 1.0 H A:GLN61 3.3 27.1 1.0 CG A:ASP59 3.3 28.2 1.0 C A:GLN61 3.4 23.4 1.0 H A:ASP59 3.5 26.5 1.0 OD2 A:ASP59 3.7 30.2 1.0 HB2 A:GLN61 3.8 35.3 1.0 N A:GLN61 4.0 22.6 1.0 HA A:PHE62 4.0 24.4 1.0 O A:HOH634 4.0 33.5 1.0 H A:ALA58 4.1 25.3 1.0 CA A:GLN61 4.2 23.8 1.0 N A:ASP59 4.3 22.1 1.0 CB A:ASP57 4.3 19.4 1.0 H A:ASN60 4.3 28.1 1.0 CB A:GLN61 4.4 29.4 1.0 N A:PHE62 4.5 21.8 1.0 CB A:ASP59 4.6 24.9 1.0 O A:HOH534 4.6 19.8 1.0 OD2 A:ASP67 4.6 19.6 1.0 N A:ALA58 4.6 21.1 1.0 N A:ASN60 4.6 23.4 1.0 O A:HOH745 4.7 34.2 1.0 HB2 A:ASP57 4.7 23.3 1.0 CA A:PHE62 4.7 20.3 1.0 H A:PHE63 4.7 26.7 1.0 HB3 A:ASP57 4.8 23.3 1.0 CA A:ASP59 4.8 24.4 1.0 HA A:ASP57 4.9 22.9 1.0 C A:ASP59 4.9 25.8 1.0 HB3 A:ALA58 4.9 29.9 1.0 HB3 A:GLN61 5.0 35.3 1.0

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


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% Mpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:23.2 occ:1.00 O A:ILE197 2.2 32.5 1.0 O A:TYR193 2.3 20.0 1.0 OG1 A:THR194 2.3 24.4 1.0 OD1 A:ASP200 2.4 20.4 1.0 O A:HOH686 2.4 28.2 1.0 O A:HOH559 2.4 22.9 1.0 O A:THR194 2.4 24.4 1.0 C A:THR194 3.2 23.1 1.0 C A:TYR193 3.4 19.8 1.0 CG A:ASP200 3.4 22.5 1.0 C A:ILE197 3.4 34.8 1.0 HB A:ILE197 3.4 44.5 1.0 CB A:THR194 3.5 24.8 1.0 H A:ILE197 3.6 49.0 1.0 CA A:THR194 3.7 24.8 1.0 OD2 A:ASP200 3.8 24.9 1.0 HB A:THR194 3.8 29.8 1.0 H A:ASP200 3.8 29.6 1.0 N A:THR194 3.9 22.4 1.0 CA A:ILE197 4.2 35.7 1.0 HA A:SER198 4.2 42.3 1.0 CB A:ILE197 4.2 37.1 1.0 N A:ILE197 4.2 40.9 1.0 HB3 A:TYR193 4.2 23.6 1.0 N A:PRO195 4.3 23.4 1.0 HA A:PRO195 4.3 32.3 1.0 HD2 A:TYR193 4.4 28.0 1.0 HG22 A:ILE197 4.4 46.6 1.0 O A:HOH582 4.5 48.8 1.0 O A:ASP200 4.5 20.6 1.0 N A:SER198 4.5 31.8 1.0 O A:GLU190 4.5 19.6 1.0 O A:HOH699 4.5 39.9 1.0 O A:HOH576 4.6 55.5 1.0 CA A:TYR193 4.6 19.5 1.0 N A:ASP200 4.6 24.7 1.0 HA A:THR194 4.6 29.8 1.0 CA A:PRO195 4.7 26.9 1.0 CG2 A:THR194 4.7 25.2 1.0 CA A:SER198 4.7 35.3 1.0 H A:THR194 4.7 26.9 1.0 CB A:ASP200 4.7 22.8 1.0 C A:ASP200 4.8 19.4 1.0 H A:GLY199 4.8 38.5 1.0 HG23 A:THR194 4.8 30.3 1.0 CB A:TYR193 4.8 19.6 1.0 CD2 A:TYR193 4.9 23.4 1.0 H A:TYR193 4.9 21.9 1.0 CG2 A:ILE197 4.9 38.9 1.0 HG21 A:THR194 5.0 30.3 1.0 CA A:ASP200 5.0 21.4 1.0 C A:SER198 5.0 34.0 1.0 C A:PRO195 5.0 32.2 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