Calcium in PDB 6d5o: Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf

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

The structure of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf, PDB code: 6d5o 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)	13.97 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.931, 93.931, 131.656, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 19.3

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

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf (pdb code 6d5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf, PDB code: 6d5o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:15.5 occ:1.00 O A:GLU187 2.3 14.9 1.0 OE1 A:GLU177 2.4 17.1 1.0 O A:HOH549 2.5 12.4 1.0 OD1 A:ASP185 2.5 15.7 1.0 OD2 A:ASP138 2.5 14.4 1.0 OE1 A:GLU190 2.6 15.8 1.0 OE2 A:GLU190 2.6 15.6 1.0 OE2 A:GLU177 2.8 16.2 1.0 CD A:GLU190 2.9 15.9 1.0 CD A:GLU177 3.0 20.1 1.0 C A:GLU187 3.4 13.1 1.0 CG A:ASP138 3.5 25.3 1.0 CG A:ASP185 3.5 19.0 1.0 HB3 A:ASP138 3.6 14.6 1.0 HA A:ILE188 3.7 13.9 1.0 H A:GLU187 3.7 20.9 1.0 CA A:CA407 3.8 17.2 1.0 OD2 A:ASP185 3.8 14.4 1.0 H A:GLY189 3.8 13.7 1.0 HB2 A:GLU187 3.9 20.0 1.0 CB A:ASP138 4.1 14.6 1.0 H A:GLU190 4.1 15.0 1.0 N A:GLU187 4.2 20.9 1.0 N A:ILE188 4.2 13.0 1.0 H A:ASP185 4.2 15.8 1.0 O A:ASP185 4.2 18.3 1.0 CA A:GLU187 4.3 20.6 1.0 HD13 A:ILE188 4.3 19.1 1.0 O A:HOH599 4.3 34.2 1.0 HB2 A:ASP138 4.3 14.6 1.0 CA A:ILE188 4.3 13.9 1.0 CG A:GLU190 4.4 20.8 1.0 OD1 A:ASP138 4.4 18.9 1.0 CG A:GLU177 4.4 12.7 1.0 N A:GLY189 4.5 13.7 1.0 O A:HOH579 4.6 15.5 1.0 CB A:GLU187 4.6 20.0 1.0 HG3 A:GLU190 4.6 20.8 1.0 C A:ASP185 4.6 11.5 1.0 HB2 A:GLU177 4.7 15.3 1.0 CB A:ASP185 4.8 20.5 1.0 N A:ASP185 4.8 15.8 1.0 C A:ILE188 4.8 17.1 1.0 HB3 A:GLU177 4.8 15.3 1.0 O A:HOH510 4.8 19.8 1.0 HG2 A:GLU190 4.9 20.8 1.0 HA A:THR174 4.9 14.1 1.0 HG2 A:GLU177 4.9 12.7 1.0 HG3 A:GLU177 4.9 12.7 1.0 HB3 A:GLU190 4.9 13.7 1.0 CB A:GLU177 5.0 15.3 1.0 N A:GLU190 5.0 15.0 1.0 H A:ILE188 5.0 13.0 1.0

Calcium binding site 2 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:16.4 occ:1.00 O A:GLN61 2.2 15.2 1.0 O A:HOH627 2.3 20.6 1.0 OD1 A:ASP57 2.4 17.1 1.0 OD1 A:ASP59 2.4 19.4 1.0 O A:HOH513 2.5 15.0 1.0 O A:HOH519 2.5 19.5 1.0 OD2 A:ASP57 2.6 15.1 1.0 CG A:ASP57 2.8 18.3 1.0 H A:GLN61 3.3 15.1 1.0 CG A:ASP59 3.4 26.9 1.0 C A:GLN61 3.4 16.6 1.0 H A:ASP59 3.6 15.4 1.0 OD2 A:ASP59 3.7 21.9 1.0 HB2 A:GLN61 3.8 18.4 1.0 O A:HOH588 3.8 33.1 1.0 HA A:PHE62 4.0 19.3 1.0 N A:GLN61 4.0 15.1 1.0 H A:ALA58 4.1 14.3 1.0 CA A:GLN61 4.1 18.1 1.0 CB A:ASP57 4.3 14.0 1.0 N A:ASP59 4.4 15.4 1.0 CB A:GLN61 4.4 18.4 1.0 N A:PHE62 4.5 16.8 1.0 H A:ASN60 4.5 19.0 1.0 OD2 A:ASP67 4.6 18.4 1.0 CB A:ASP59 4.7 14.2 1.0 O A:HOH535 4.7 13.6 1.0 N A:ALA58 4.7 14.3 1.0 CA A:PHE62 4.7 19.3 1.0 HB2 A:ASP57 4.7 14.0 1.0 N A:ASN60 4.7 19.0 1.0 H A:PHE63 4.8 14.2 1.0 HB3 A:ASP57 4.8 14.0 1.0 HB3 A:GLN61 4.9 18.4 1.0 CA A:ASP59 4.9 18.9 1.0 HA A:ASP57 4.9 12.3 1.0 C A:ASP59 4.9 16.0 1.0 HB3 A:ALA58 5.0 17.8 1.0

Calcium binding site 3 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:18.5 occ:1.00 OG1 A:THR194 2.3 21.5 1.0 OD1 A:ASP200 2.3 19.9 1.0 O A:TYR193 2.3 14.0 1.0 O A:ILE197 2.4 26.5 1.0 O A:HOH514 2.4 20.1 1.0 O A:HOH607 2.4 23.8 1.0 O A:THR194 2.4 24.0 1.0 C A:THR194 3.3 25.6 1.0 CG A:ASP200 3.4 21.2 1.0 C A:TYR193 3.4 18.6 1.0 CB A:THR194 3.5 21.1 1.0 C A:ILE197 3.5 29.3 1.0 HB A:ILE197 3.6 28.8 1.0 H A:ILE197 3.6 27.8 1.0 OD2 A:ASP200 3.7 22.1 1.0 CA A:THR194 3.7 15.9 1.0 HB A:THR194 3.8 21.1 1.0 H A:ASP200 3.9 24.4 1.0 N A:THR194 3.9 18.0 1.0 HB3 A:TYR193 4.1 15.8 1.0 HD2 A:TYR193 4.2 24.1 1.0 HA A:SER198 4.2 35.1 1.0 CA A:ILE197 4.3 25.5 1.0 HA A:PRO195 4.3 21.8 1.0 N A:ILE197 4.3 27.8 1.0 N A:PRO195 4.3 19.1 1.0 CB A:ILE197 4.3 28.8 1.0 O A:ASP200 4.4 21.2 1.0 O A:GLU190 4.5 16.5 1.0 CA A:TYR193 4.5 16.5 1.0 HG22 A:ILE197 4.6 33.8 1.0 N A:SER198 4.6 33.6 1.0 HA A:THR194 4.7 15.9 1.0 N A:ASP200 4.7 24.4 1.0 CA A:PRO195 4.7 21.8 1.0 CG2 A:THR194 4.7 22.3 1.0 CB A:ASP200 4.7 17.4 1.0 CB A:TYR193 4.7 15.8 1.0 C A:ASP200 4.8 27.2 1.0 H A:THR194 4.8 18.0 1.0 CD2 A:TYR193 4.8 24.1 1.0 HG23 A:THR194 4.8 22.3 1.0 CA A:SER198 4.8 35.1 1.0 H A:GLY199 4.8 24.5 1.0 H A:TYR193 4.8 14.7 1.0 HG21 A:THR194 4.9 22.3 1.0 CA A:ASP200 5.0 21.0 1.0 C A:PRO195 5.0 31.8 1.0 N A:TYR193 5.0 14.7 1.0

Calcium binding site 4 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:17.2 occ:1.00 OE2 A:GLU190 2.3 15.6 1.0 OD2 A:ASP185 2.3 14.4 1.0 O A:ASN183 2.3 19.2 1.0 OE2 A:GLU177 2.4 16.2 1.0 O A:HOH510 2.4 19.8 1.0 O A:HOH571 2.4 18.1 1.0 CG A:ASP185 3.2 19.0 1.0 CD A:GLU177 3.2 20.1 1.0 CD A:GLU190 3.3 15.9 1.0 C A:ASN183 3.5 17.4 1.0 HG3 A:GLU190 3.6 20.8 1.0 OD1 A:ASP185 3.6 15.7 1.0 HA A:PRO184 3.7 21.6 1.0 HB3 A:ASN183 3.7 25.9 1.0 CA A:CA404 3.8 15.5 1.0 OE1 A:GLU177 3.8 17.1 1.0 O A:LYS182 3.8 25.5 1.0 CG A:GLU190 3.8 20.8 1.0 HB2 A:ASN183 3.8 25.9 1.0 HG2 A:GLU190 3.8 20.8 1.0 H A:ASP185 4.0 15.8 1.0 CB A:ASN183 4.2 25.9 1.0 N A:ASP185 4.2 15.8 1.0 CA A:PRO184 4.2 21.6 1.0 HG2 A:GLU177 4.3 12.7 1.0 C A:PRO184 4.3 25.5 1.0 OD1 A:ASP191 4.3 17.1 1.0 CG A:GLU177 4.3 12.7 1.0 OE1 A:GLU190 4.3 15.8 1.0 HB3 A:ASP185 4.3 20.5 1.0 OD2 A:ASP191 4.3 21.0 1.0 N A:PRO184 4.3 21.4 1.0 CB A:ASP185 4.3 20.5 1.0 HG3 A:GLU177 4.4 12.7 1.0 CA A:ASN183 4.4 19.4 1.0 O A:HOH599 4.5 34.2 1.0 CG A:ASP191 4.6 25.3 1.0 C A:LYS182 4.9 24.1 1.0 CA A:ASP185 4.9 13.7 1.0 O A:PRO184 4.9 21.3 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