Calcium in PDB 5wr6: Thermolysin, Liganded Form with Cryo Condition 2

All present enzymatic activity of Thermolysin, Liganded Form with Cryo Condition 2:
3.4.24.27;

The structure of Thermolysin, Liganded Form with Cryo Condition 2, PDB code: 5wr6 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)	40.20 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.929, 92.929, 129.140, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 18.2

The structure of Thermolysin, Liganded Form with Cryo Condition 2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin, Liganded Form with Cryo Condition 2 (pdb code 5wr6). 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 2, PDB code: 5wr6:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.6 occ:1.00 O A:GLN61 2.2 14.8 1.0 OD2 A:ASP57 2.4 16.4 1.0 OD1 A:ASP59 2.4 19.9 1.0 O A:HOH744 2.5 21.4 1.0 O A:HOH549 2.5 14.3 1.0 OD1 A:ASP57 2.6 16.7 1.0 O A:HOH584 2.8 26.8 1.0 CG A:ASP57 2.8 16.7 1.0 C A:GLN61 3.3 17.3 1.0 CG A:ASP59 3.4 20.5 1.0 OD2 A:ASP59 3.8 26.5 1.0 N A:GLN61 3.8 18.4 1.0 O A:HOH563 3.8 19.8 1.0 CA A:GLN61 3.9 19.7 1.0 CB A:GLN61 4.0 26.4 1.0 N A:ASP59 4.3 18.5 1.0 CB A:ASP57 4.3 12.8 1.0 N A:PHE62 4.4 17.0 1.0 O A:HOH531 4.5 14.2 1.0 OD2 A:ASP67 4.6 17.2 1.0 CA A:PHE62 4.7 16.6 1.0 CB A:ASP59 4.7 20.2 1.0 O A:HOH668 4.7 20.5 1.0 N A:ALA58 4.7 15.6 1.0 N A:ASN60 4.8 18.9 1.0 CA A:ASP59 4.8 18.2 1.0 O A:HOH919 4.8 30.2 1.0 C A:ASP59 4.9 19.7 1.0 C A:ASN60 5.0 19.7 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:14.2 occ:1.00 O A:GLU187 2.3 13.1 1.0 OE2 A:GLU190 2.5 16.4 1.0 OE1 A:GLU190 2.5 17.7 1.0 O A:HOH567 2.5 18.1 1.0 OD2 A:ASP138 2.5 20.3 1.0 OD1 A:ASP185 2.6 18.9 1.0 OE1 A:GLU177 2.6 17.9 1.0 OE2 A:GLU177 2.7 18.9 1.0 CD A:GLU190 2.8 18.7 1.0 CD A:GLU177 3.0 21.5 1.0 C A:GLU187 3.4 19.2 1.0 CG A:ASP138 3.4 15.6 1.0 CG A:ASP185 3.5 24.3 1.0 CA A:CA405 3.9 22.5 1.0 OD2 A:ASP185 3.9 20.6 1.0 O A:HOH504 3.9 29.7 1.0 CB A:ASP138 4.0 13.5 1.0 O A:ASP185 4.1 19.3 1.0 N A:ILE188 4.2 20.3 1.0 CA A:ILE188 4.2 17.5 1.0 OD1 A:ASP138 4.3 16.2 1.0 N A:GLU187 4.3 18.6 1.0 CG A:GLU190 4.3 17.6 1.0 CA A:GLU187 4.3 23.8 1.0 N A:GLY189 4.4 17.4 1.0 O A:HOH557 4.4 18.7 1.0 CG A:GLU177 4.5 18.6 1.0 C A:ASP185 4.6 25.7 1.0 CB A:GLU187 4.7 24.6 1.0 C A:ILE188 4.7 19.7 1.0 N A:ASP185 4.8 20.3 1.0 CB A:ASP185 4.8 26.1 1.0 N A:GLU190 4.9 15.4 1.0 CA A:ASP185 5.0 20.9 1.0 CB A:GLU177 5.0 15.8 1.0

Calcium binding site 3 out of 4 in the Thermolysin, Liganded Form with Cryo Condition 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:22.5 occ:1.00 O A:ASN183 2.3 22.1 1.0 O A:HOH666 2.3 19.8 1.0 OE2 A:GLU190 2.4 16.4 1.0 O A:HOH602 2.5 25.3 1.0 OD2 A:ASP185 2.6 20.6 1.0 OE2 A:GLU177 2.6 18.9 1.0 CD A:GLU190 3.2 18.7 1.0 CG A:ASP185 3.4 24.3 1.0 CD A:GLU177 3.4 21.5 1.0 C A:ASN183 3.5 25.2 1.0 CG A:GLU190 3.7 17.6 1.0 OD1 A:ASP185 3.8 18.9 1.0 OE1 A:GLU177 3.8 17.9 1.0 CA A:CA404 3.9 14.2 1.0 CB A:ASN183 4.1 27.9 1.0 OD1 A:ASP191 4.1 18.6 1.0 CA A:PRO184 4.2 22.2 1.0 N A:ASP185 4.2 20.3 1.0 OE1 A:GLU190 4.2 17.7 1.0 C A:PRO184 4.3 24.6 1.0 O A:HOH504 4.3 29.7 1.0 CG A:GLU177 4.3 18.6 1.0 OD2 A:ASP191 4.4 18.4 1.0 N A:PRO184 4.4 23.5 1.0 CB A:ASP185 4.4 26.1 1.0 O A:LYS182 4.4 29.3 1.0 O A:HOH888 4.5 33.0 1.0 CA A:ASN183 4.5 31.9 1.0 O A:HOH781 4.5 40.8 1.0 CG A:ASP191 4.6 19.4 1.0 O A:PRO184 4.9 26.0 1.0 CA A:ASP185 4.9 20.9 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:24.1 occ:1.00 O A:ILE197 2.3 38.5 1.0 OG1 A:THR194 2.3 20.2 1.0 O A:THR194 2.3 24.7 1.0 OD1 A:ASP200 2.4 23.5 1.0 O A:TYR193 2.4 21.3 1.0 O A:HOH511 2.6 19.0 1.0 O A:HOH731 2.6 24.0 1.0 C A:THR194 3.2 24.2 1.0 C A:TYR193 3.4 19.3 1.0 CG A:ASP200 3.4 26.1 1.0 C A:ILE197 3.5 35.4 1.0 CB A:THR194 3.5 27.2 1.0 CA A:THR194 3.7 24.8 1.0 OD2 A:ASP200 3.8 29.2 1.0 N A:THR194 3.9 19.2 1.0 O A:HOH765 4.2 38.6 1.0 CA A:ILE197 4.2 32.4 1.0 N A:PRO195 4.2 26.2 1.0 N A:ILE197 4.3 38.4 1.0 CB A:ILE197 4.3 40.8 1.0 O A:ASP200 4.4 20.0 1.0 N A:SER198 4.5 37.3 1.0 O A:GLU190 4.6 19.1 1.0 CA A:TYR193 4.6 20.6 1.0 CA A:SER198 4.6 38.5 1.0 CA A:PRO195 4.6 28.6 1.0 O A:HOH686 4.7 27.6 1.0 CD2 A:TYR193 4.7 20.2 1.0 CG2 A:THR194 4.7 21.8 1.0 N A:ASP200 4.7 23.4 1.0 O A:HOH706 4.7 34.1 1.0 CB A:TYR193 4.7 18.1 1.0 CB A:ASP200 4.7 25.9 1.0 C A:ASP200 4.8 23.6 1.0 C A:SER198 4.9 34.8 1.0 C A:PRO195 5.0 34.8 1.0 CA A:ASP200 5.0 22.9 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