Calcium in PDB 6d5n: Hexagonal Thermolysin (295) in the Presence of 50% Xylose

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

The structure of Hexagonal Thermolysin (295) in the Presence of 50% Xylose, PDB code: 6d5n 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)	13.85 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.803, 93.803, 132.293, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 18.7

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

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Hexagonal Thermolysin (295) in the Presence of 50% Xylose (pdb code 6d5n). 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) in the Presence of 50% Xylose, PDB code: 6d5n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Hexagonal Thermolysin (295) 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 Hexagonal Thermolysin (295) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:14.7 occ:1.00 O A:GLU187 2.3 13.1 1.0 OE1 A:GLU177 2.4 14.7 1.0 OE2 A:GLU190 2.5 13.9 1.0 O A:HOH570 2.5 12.0 1.0 OD2 A:ASP138 2.5 15.5 1.0 OD1 A:ASP185 2.5 15.1 1.0 OE1 A:GLU190 2.6 12.5 1.0 OE2 A:GLU177 2.8 14.9 1.0 CD A:GLU190 2.8 17.2 1.0 CD A:GLU177 3.0 21.7 1.0 C A:GLU187 3.4 12.7 1.0 CG A:ASP138 3.5 16.4 1.0 CG A:ASP185 3.5 19.3 1.0 HB3 A:ASP138 3.6 18.6 1.0 HA A:ILE188 3.7 14.6 1.0 H A:GLU187 3.7 22.3 1.0 CA A:CA407 3.8 16.5 1.0 H A:GLY189 3.8 13.8 1.0 OD2 A:ASP185 3.9 17.1 1.0 HB2 A:GLU187 3.9 22.7 1.0 CB A:ASP138 4.1 15.5 1.0 H A:GLU190 4.1 15.2 1.0 N A:ILE188 4.2 11.3 1.0 HD13 A:ILE188 4.2 21.2 1.0 N A:GLU187 4.3 18.6 1.0 H A:ASP185 4.3 18.8 1.0 O A:ASP185 4.3 15.9 1.0 HB2 A:ASP138 4.3 18.6 1.0 CA A:GLU187 4.3 15.4 1.0 CA A:ILE188 4.3 12.2 1.0 CG A:GLU190 4.3 19.6 1.0 OD1 A:ASP138 4.4 15.3 1.0 CG A:GLU177 4.4 13.8 1.0 N A:GLY189 4.4 11.5 1.0 O A:HOH559 4.5 18.1 1.0 HG3 A:GLU190 4.6 23.6 1.0 CB A:GLU187 4.6 18.9 1.0 HB2 A:GLU177 4.7 21.7 1.0 C A:ASP185 4.7 15.3 1.0 HG2 A:GLU190 4.8 23.6 1.0 C A:ILE188 4.8 14.3 1.0 CB A:ASP185 4.8 19.5 1.0 HB3 A:GLU177 4.8 21.7 1.0 HA A:THR174 4.8 17.2 1.0 N A:ASP185 4.8 15.7 1.0 HG2 A:GLU177 4.9 16.5 1.0 O A:HOH508 4.9 18.2 1.0 HG3 A:GLU177 4.9 16.5 1.0 N A:GLU190 4.9 12.7 1.0 CB A:GLU177 4.9 18.1 1.0 HB3 A:GLU190 4.9 16.0 1.0

Calcium binding site 2 out of 4 in the Hexagonal Thermolysin (295) 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 Hexagonal Thermolysin (295) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:15.3 occ:1.00 O A:GLN61 2.2 15.5 1.0 OD1 A:ASP59 2.4 19.4 1.0 O A:HOH512 2.4 13.2 1.0 O A:HOH629 2.4 18.8 1.0 O A:HOH525 2.4 18.4 1.0 OD1 A:ASP57 2.5 16.4 1.0 OD2 A:ASP57 2.5 15.1 1.0 CG A:ASP57 2.8 15.4 1.0 H A:GLN61 3.3 16.1 1.0 CG A:ASP59 3.3 25.6 1.0 C A:GLN61 3.4 13.1 1.0 H A:ASP59 3.6 17.7 1.0 OD2 A:ASP59 3.7 20.7 1.0 HB2 A:GLN61 3.8 19.9 1.0 N A:GLN61 4.0 13.4 1.0 HA A:PHE62 4.0 16.5 1.0 O A:HOH587 4.0 22.8 1.0 CA A:GLN61 4.1 16.1 1.0 H A:ALA58 4.1 20.6 1.0 CB A:ASP57 4.3 16.3 1.0 N A:ASP59 4.4 14.7 1.0 O A:HOH615 4.4 21.3 1.0 CB A:GLN61 4.4 16.6 1.0 N A:PHE62 4.4 15.4 1.0 H A:ASN60 4.5 22.4 1.0 OD2 A:ASP67 4.6 15.6 1.0 CB A:ASP59 4.6 16.6 1.0 O A:HOH515 4.7 11.0 1.0 CA A:PHE62 4.7 13.8 1.0 N A:ALA58 4.7 17.2 1.0 N A:ASN60 4.7 18.7 1.0 HB2 A:ASP57 4.7 19.6 1.0 H A:PHE63 4.7 16.5 1.0 HB3 A:ASP57 4.8 19.6 1.0 CA A:ASP59 4.8 16.2 1.0 HB3 A:GLN61 4.9 19.9 1.0 C A:ASP59 4.9 18.3 1.0 HA A:ASP57 4.9 20.3 1.0 O A:HOH635 4.9 33.3 1.0

Calcium binding site 3 out of 4 in the Hexagonal Thermolysin (295) 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 Hexagonal Thermolysin (295) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:19.7 occ:1.00 O A:ILE197 2.3 29.0 1.0 OD1 A:ASP200 2.3 20.1 1.0 O A:HOH595 2.3 22.8 1.0 O A:TYR193 2.3 14.7 1.0 O A:HOH520 2.4 15.4 1.0 OG1 A:THR194 2.4 21.8 1.0 O A:THR194 2.4 22.1 1.0 C A:THR194 3.3 22.0 1.0 CG A:ASP200 3.4 18.2 1.0 C A:TYR193 3.4 16.9 1.0 CB A:THR194 3.5 21.6 1.0 C A:ILE197 3.5 25.6 1.0 H A:ILE197 3.7 39.0 1.0 HB A:ILE197 3.7 34.8 1.0 OD2 A:ASP200 3.7 22.4 1.0 CA A:THR194 3.7 13.6 1.0 HB A:THR194 3.7 25.9 1.0 H A:ASP200 3.8 25.2 1.0 N A:THR194 3.9 18.1 1.0 HA A:SER198 4.1 30.9 1.0 HD2 A:TYR193 4.1 22.4 1.0 HB3 A:TYR193 4.2 23.3 1.0 HA A:PRO195 4.3 28.8 1.0 CA A:ILE197 4.3 26.9 1.0 N A:PRO195 4.3 20.5 1.0 N A:ILE197 4.3 32.5 1.0 O A:ASP200 4.3 18.6 1.0 CB A:ILE197 4.4 29.0 1.0 N A:SER198 4.5 30.2 1.0 O A:GLU190 4.5 20.4 1.0 HG22 A:ILE197 4.5 36.8 1.0 CA A:TYR193 4.6 17.8 1.0 N A:ASP200 4.6 21.0 1.0 HA A:THR194 4.7 16.3 1.0 CA A:SER198 4.7 25.7 1.0 CD2 A:TYR193 4.7 18.7 1.0 CA A:PRO195 4.7 24.0 1.0 CB A:ASP200 4.7 15.5 1.0 C A:ASP200 4.7 21.7 1.0 CB A:TYR193 4.8 19.4 1.0 CG2 A:THR194 4.8 18.6 1.0 H A:THR194 4.8 21.7 1.0 H A:TYR193 4.8 18.0 1.0 H A:GLY199 4.8 30.2 1.0 HG23 A:THR194 4.9 22.3 1.0 CA A:ASP200 4.9 19.0 1.0 C A:SER198 5.0 21.1 1.0 HG21 A:THR194 5.0 22.3 1.0

Calcium binding site 4 out of 4 in the Hexagonal Thermolysin (295) 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 4 of Hexagonal Thermolysin (295) in the Presence of 50% Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:16.5 occ:1.00 OE2 A:GLU190 2.3 13.9 1.0 OE2 A:GLU177 2.4 14.9 1.0 O A:ASN183 2.4 19.4 1.0 O A:HOH508 2.4 18.2 1.0 OD2 A:ASP185 2.4 17.1 1.0 O A:HOH558 2.4 18.8 1.0 CG A:ASP185 3.2 19.3 1.0 CD A:GLU177 3.2 21.7 1.0 CD A:GLU190 3.3 17.2 1.0 C A:ASN183 3.5 19.6 1.0 OD1 A:ASP185 3.6 15.1 1.0 HG3 A:GLU190 3.6 23.6 1.0 HA A:PRO184 3.6 18.3 1.0 OE1 A:GLU177 3.7 14.7 1.0 CA A:CA404 3.8 14.7 1.0 HB2 A:ASN183 3.8 27.7 1.0 HG2 A:GLU190 3.8 23.6 1.0 CG A:GLU190 3.8 19.6 1.0 O A:LYS182 3.8 24.7 1.0 HB3 A:ASN183 4.0 27.7 1.0 H A:ASP185 4.1 18.8 1.0 CA A:PRO184 4.2 15.2 1.0 N A:ASP185 4.2 15.7 1.0 OD2 A:ASP191 4.2 20.9 1.0 HG2 A:GLU177 4.2 16.5 1.0 CG A:GLU177 4.2 13.8 1.0 OD1 A:ASP191 4.2 17.1 1.0 CB A:ASN183 4.2 23.1 1.0 C A:PRO184 4.3 22.9 1.0 OE1 A:GLU190 4.3 12.5 1.0 N A:PRO184 4.3 17.8 1.0 HB3 A:ASP185 4.3 23.4 1.0 HG3 A:GLU177 4.3 16.5 1.0 CB A:ASP185 4.3 19.5 1.0 O A:HOH548 4.4 34.1 1.0 CA A:ASN183 4.5 21.9 1.0 CG A:ASP191 4.6 19.1 1.0 C A:LYS182 4.9 23.4 1.0 O A:PRO184 4.9 23.4 1.0 CA A:ASP185 4.9 17.4 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