Calcium in PDB 5wr5: Thermolysin, Liganded Form with Cryo Condition 1

All present enzymatic activity of Thermolysin, Liganded Form with Cryo Condition 1:
3.4.24.27;

The structure of Thermolysin, Liganded Form with Cryo Condition 1, PDB code: 5wr5 was solved by N.Kunishima, H.Naitow, Y.Matsuura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.246, 92.246, 129.718, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 19

The structure of Thermolysin, Liganded Form with Cryo Condition 1 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin, Liganded Form with Cryo Condition 1 (pdb code 5wr5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin, Liganded Form with Cryo Condition 1, PDB code: 5wr5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin, Liganded Form with Cryo Condition 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin, Liganded Form with Cryo Condition 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:18.0 occ:1.00 O A:GLN61 2.3 17.9 1.0 OD1 A:ASP57 2.4 15.8 1.0 OD1 A:ASP59 2.4 22.0 1.0 O A:HOH724 2.4 20.5 1.0 O A:HOH597 2.4 21.2 1.0 O A:HOH591 2.5 17.6 1.0 OD2 A:ASP57 2.5 16.8 1.0 CG A:ASP57 2.8 19.4 1.0 CG A:ASP59 3.4 21.8 1.0 C A:GLN61 3.4 14.2 1.0 OD2 A:ASP59 3.7 22.2 1.0 O A:HOH609 4.0 27.9 1.0 N A:GLN61 4.0 18.6 1.0 CA A:GLN61 4.1 17.2 1.0 CB A:ASP57 4.3 16.2 1.0 N A:ASP59 4.3 17.6 1.0 CB A:GLN61 4.4 23.5 1.0 N A:PHE62 4.5 14.5 1.0 O A:HOH651 4.5 18.3 1.0 N A:ALA58 4.6 19.2 1.0 OD2 A:ASP67 4.6 16.8 1.0 O A:HOH524 4.6 19.9 1.0 CB A:ASP59 4.7 22.4 1.0 CA A:PHE62 4.7 15.4 1.0 N A:ASN60 4.7 17.8 1.0 CA A:ASP59 4.8 23.7 1.0 O A:HOH861 4.9 32.9 1.0 C A:ASP59 4.9 22.6 1.0

Calcium binding site 2 out of 4 in the Thermolysin, Liganded Form with Cryo Condition 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin, Liganded Form with Cryo Condition 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:16.0 occ:1.00 O A:GLU187 2.4 15.8 1.0 OD2 A:ASP138 2.4 14.8 1.0 O A:HOH622 2.4 14.0 1.0 OE2 A:GLU190 2.5 20.2 1.0 OD1 A:ASP185 2.5 14.1 1.0 OE1 A:GLU177 2.5 17.2 1.0 OE1 A:GLU190 2.5 17.4 1.0 OE2 A:GLU177 2.8 20.0 1.0 CD A:GLU190 2.8 16.5 1.0 CD A:GLU177 3.0 19.2 1.0 C A:GLU187 3.4 14.5 1.0 CG A:ASP138 3.4 16.9 1.0 CG A:ASP185 3.5 19.0 1.0 OD2 A:ASP185 3.8 20.0 1.0 CA A:CA405 3.9 20.2 1.0 CB A:ASP138 4.1 11.0 1.0 O A:ASP185 4.1 17.8 1.0 N A:GLU187 4.2 17.4 1.0 N A:ILE188 4.2 13.1 1.0 CA A:ILE188 4.3 13.5 1.0 CA A:GLU187 4.3 14.8 1.0 CG A:GLU190 4.3 15.8 1.0 OD1 A:ASP138 4.4 21.1 1.0 O A:HOH642 4.4 17.2 0.7 N A:GLY189 4.4 15.3 1.0 CG A:GLU177 4.4 12.7 1.0 O A:HOH575 4.5 21.6 1.0 C A:ASP185 4.6 19.9 1.0 CB A:GLU187 4.7 18.1 1.0 N A:ASP185 4.8 14.1 1.0 CB A:ASP185 4.8 19.3 1.0 C A:ILE188 4.8 15.4 1.0 O A:HOH521 4.8 18.1 1.0 CB A:GLU177 4.9 15.3 1.0 CA A:ASP185 5.0 21.3 1.0

Calcium binding site 3 out of 4 in the Thermolysin, Liganded Form with Cryo Condition 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin, Liganded Form with Cryo Condition 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:20.2 occ:1.00 O A:ASN183 2.3 19.9 1.0 O A:HOH521 2.3 18.1 1.0 OE2 A:GLU190 2.4 20.2 1.0 O A:HOH543 2.4 20.3 1.0 OD2 A:ASP185 2.4 20.0 1.0 OE2 A:GLU177 2.4 20.0 1.0 CG A:ASP185 3.2 19.0 1.0 CD A:GLU177 3.2 19.2 1.0 CD A:GLU190 3.4 16.5 1.0 C A:ASN183 3.5 23.6 1.0 OD1 A:ASP185 3.6 14.1 1.0 OE1 A:GLU177 3.8 17.2 1.0 CG A:GLU190 3.9 15.8 1.0 CA A:CA404 3.9 16.0 1.0 O A:LYS182 4.1 27.6 1.0 CB A:ASN183 4.1 24.6 1.0 OD1 A:ASP191 4.1 22.7 1.0 OD2 A:ASP191 4.1 23.0 1.0 CA A:PRO184 4.2 19.9 1.0 N A:ASP185 4.2 14.1 1.0 C A:PRO184 4.2 25.3 1.0 CG A:GLU177 4.2 12.7 1.0 N A:PRO184 4.3 23.7 1.0 CB A:ASP185 4.3 19.3 1.0 OE1 A:GLU190 4.4 17.4 1.0 CA A:ASN183 4.4 24.7 1.0 CG A:ASP191 4.4 22.2 1.0 O A:HOH842 4.6 36.7 1.0 O A:HOH642 4.7 17.2 0.7 O A:PRO184 4.9 20.8 1.0 CA A:ASP185 4.9 21.3 1.0

Calcium binding site 4 out of 4 in the Thermolysin, Liganded Form with Cryo Condition 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin, Liganded Form with Cryo Condition 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:20.8 occ:1.00 O A:ILE197 2.3 26.6 1.0 OG1 A:THR194 2.3 23.3 1.0 O A:THR194 2.3 25.8 1.0 O A:TYR193 2.4 19.5 1.0 O A:HOH700 2.4 29.1 1.0 OD1 A:ASP200 2.4 20.3 1.0 O A:HOH532 2.4 20.7 1.0 C A:THR194 3.2 23.5 1.0 C A:TYR193 3.3 17.6 1.0 CB A:THR194 3.4 19.8 1.0 C A:ILE197 3.5 35.4 1.0 CG A:ASP200 3.5 19.9 1.0 CA A:THR194 3.6 22.6 1.0 N A:THR194 3.9 20.8 1.0 OD2 A:ASP200 3.9 20.8 1.0 CA A:ILE197 4.2 27.6 1.0 CB A:ILE197 4.2 29.6 1.0 N A:PRO195 4.3 25.9 1.0 O A:HOH685 4.3 46.0 1.0 N A:ILE197 4.3 26.2 1.0 O A:ASP200 4.4 24.8 1.0 O A:HOH673 4.4 38.2 1.0 N A:SER198 4.5 22.1 1.0 CA A:TYR193 4.5 18.8 1.0 O A:GLU190 4.6 19.8 1.0 N A:ASP200 4.6 22.3 1.0 CB A:TYR193 4.6 16.7 1.0 CA A:SER198 4.6 33.2 1.0 CA A:PRO195 4.7 28.4 1.0 CG2 A:THR194 4.7 21.7 1.0 CD2 A:TYR193 4.7 20.3 1.0 C A:ASP200 4.8 20.7 1.0 CB A:ASP200 4.8 22.6 1.0 O A:HOH663 4.8 44.7 1.0 C A:SER198 4.9 25.3 1.0 CG2 A:ILE197 4.9 30.6 1.0 CA A:ASP200 5.0 22.2 1.0 N A:GLY199 5.0 29.4 1.0 C A:PRO195 5.0 29.8 1.0 CG A:TYR193 5.0 17.0 1.0 N A:TYR193 5.0 17.4 1.0

H.Naitow, Y.Matsuura, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, R.Tanaka, T.Tanaka, M.Sugahara, J.Kobayashi, E.Nango, S.Iwata, N.Kunishima. Protein-Ligand Complex Structure From Serial Femtosecond Crystallography Using Soaked Thermolysin Microcrystals and Comparison with Structures From Synchrotron Radiation Acta Crystallogr D Struct V. 73 702 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28777085
DOI: 10.1107/S2059798317008919