Calcium in PDB 5wr4: Thermolysin, Sfx Unliganded Form with Oil-Based Carrier

All present enzymatic activity of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier:
3.4.24.27;

The structure of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier, PDB code: 5wr4 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)	46.80 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.670, 93.670, 130.950, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 18.8

The structure of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Thermolysin, Sfx Unliganded Form with Oil-Based Carrier (pdb code 5wr4). 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, Sfx Unliganded Form with Oil-Based Carrier, PDB code: 5wr4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin, Sfx Unliganded Form with Oil-Based Carrier


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:26.5 occ:1.00 O A:GLN61 2.3 25.6 1.0 O A:HOH665 2.4 25.3 1.0 OD1 A:ASP57 2.4 24.8 1.0 OD1 A:ASP59 2.4 30.8 1.0 O A:HOH527 2.5 22.1 1.0 O A:HOH563 2.5 29.9 1.0 OD2 A:ASP57 2.6 23.9 1.0 CG A:ASP57 2.9 24.8 1.0 CG A:ASP59 3.4 31.6 1.0 C A:GLN61 3.4 27.2 1.0 OD2 A:ASP59 3.7 29.1 1.0 O A:HOH571 3.9 35.8 1.0 N A:GLN61 4.0 25.4 1.0 CA A:GLN61 4.2 28.2 1.0 CB A:ASP57 4.4 24.8 1.0 N A:ASP59 4.4 24.6 1.0 O A:HOH623 4.4 31.8 1.0 CB A:GLN61 4.4 29.5 1.0 N A:PHE62 4.5 23.1 1.0 O A:HOH511 4.6 26.2 1.0 OD2 A:ASP67 4.6 25.9 1.0 CB A:ASP59 4.7 30.3 1.0 CA A:PHE62 4.7 27.7 1.0 O A:HOH761 4.8 44.9 1.0 N A:ALA58 4.8 26.3 1.0 N A:ASN60 4.8 27.7 1.0 CA A:ASP59 4.9 25.0 1.0 C A:ASP59 5.0 28.1 1.0

Calcium binding site 2 out of 4 in the Thermolysin, Sfx Unliganded Form with Oil-Based Carrier


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:24.5 occ:1.00 O A:GLU187 2.4 21.2 1.0 OE1 A:GLU177 2.4 23.4 1.0 O A:HOH585 2.4 23.2 1.0 OD2 A:ASP138 2.5 23.2 1.0 OE2 A:GLU190 2.5 21.7 1.0 OE1 A:GLU190 2.6 25.4 1.0 OD1 A:ASP185 2.6 24.5 1.0 OE2 A:GLU177 2.8 25.0 1.0 CD A:GLU190 2.9 24.8 1.0 CD A:GLU177 2.9 23.5 1.0 CG A:ASP138 3.4 26.0 1.0 C A:GLU187 3.5 27.5 1.0 CG A:ASP185 3.5 29.5 1.0 CA A:CA404 3.7 28.2 1.0 OD2 A:ASP185 3.8 25.0 1.0 CB A:ASP138 3.9 21.0 1.0 O A:HOH519 4.1 26.7 0.5 N A:GLU187 4.2 29.6 1.0 O A:ASP185 4.3 29.0 1.0 OD1 A:ASP138 4.3 26.9 1.0 N A:ILE188 4.3 24.4 1.0 CA A:GLU187 4.3 27.3 1.0 CA A:ILE188 4.4 24.1 1.0 CG A:GLU190 4.4 22.9 1.0 CG A:GLU177 4.4 20.6 1.0 N A:GLY189 4.4 23.9 1.0 O A:HOH561 4.5 28.3 1.0 CB A:GLU187 4.6 27.9 1.0 C A:ASP185 4.7 26.7 1.0 C A:ILE188 4.8 29.3 1.0 CB A:ASP185 4.9 25.6 1.0 N A:ASP185 4.9 29.4 1.0 O A:HOH514 4.9 27.0 1.0 CB A:GLU177 4.9 23.1 1.0 N A:GLU190 4.9 21.1 1.0

Calcium binding site 3 out of 4 in the Thermolysin, Sfx Unliganded Form with Oil-Based Carrier


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:28.2 occ:1.00 OE2 A:GLU190 2.3 21.7 1.0 OD2 A:ASP185 2.3 25.0 1.0 OE2 A:GLU177 2.4 25.0 1.0 O A:ASN183 2.4 26.6 1.0 O A:HOH553 2.4 30.6 1.0 O A:HOH514 2.5 27.0 1.0 CD A:GLU177 3.2 23.5 1.0 CG A:ASP185 3.2 29.5 1.0 CD A:GLU190 3.3 24.8 1.0 C A:ASN183 3.5 30.5 1.0 OD1 A:ASP185 3.7 24.5 1.0 OE1 A:GLU177 3.7 23.4 1.0 CA A:CA403 3.7 24.5 1.0 CG A:GLU190 3.8 22.9 1.0 O A:LYS182 3.9 35.8 1.0 CB A:ASN183 4.1 36.3 1.0 CG A:GLU177 4.2 20.6 1.0 N A:ASP185 4.2 29.4 1.0 OD2 A:ASP191 4.2 29.2 1.0 OD1 A:ASP191 4.2 33.1 1.0 CA A:PRO184 4.2 33.5 1.0 OE1 A:GLU190 4.3 25.4 1.0 C A:PRO184 4.3 35.0 1.0 N A:PRO184 4.4 29.8 1.0 CB A:ASP185 4.4 25.6 1.0 CA A:ASN183 4.5 28.8 1.0 O A:HOH519 4.5 26.7 0.5 CG A:ASP191 4.6 30.9 1.0 C A:LYS182 4.9 37.9 1.0 CA A:ASP185 4.9 27.5 1.0 O A:PRO184 5.0 35.6 1.0

Calcium binding site 4 out of 4 in the Thermolysin, Sfx Unliganded Form with Oil-Based Carrier


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin, Sfx Unliganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:30.1 occ:1.00 O A:HOH575 2.3 40.2 1.0 OG1 A:THR194 2.3 27.4 1.0 OD1 A:ASP200 2.3 31.4 1.0 O A:ILE197 2.3 42.3 1.0 O A:THR194 2.4 32.7 1.0 O A:TYR193 2.4 26.0 1.0 O A:HOH531 2.5 26.3 1.0 C A:THR194 3.2 33.0 1.0 CG A:ASP200 3.3 30.7 1.0 C A:TYR193 3.4 29.6 1.0 CB A:THR194 3.4 29.6 1.0 C A:ILE197 3.5 45.3 1.0 CA A:THR194 3.6 28.1 1.0 OD2 A:ASP200 3.7 31.1 1.0 N A:THR194 3.9 27.5 1.0 CA A:ILE197 4.2 36.4 1.0 N A:ILE197 4.2 44.6 1.0 CB A:ILE197 4.2 43.2 1.0 N A:PRO195 4.3 32.7 1.0 O A:ASP200 4.4 29.5 1.0 O A:GLU190 4.5 28.7 1.0 N A:SER198 4.5 41.5 1.0 CA A:TYR193 4.6 27.5 1.0 N A:ASP200 4.6 39.7 1.0 CG2 A:THR194 4.6 30.4 1.0 CB A:ASP200 4.7 30.1 1.0 C A:ASP200 4.7 29.5 1.0 O A:HOH668 4.7 39.8 1.0 CB A:TYR193 4.7 28.9 1.0 CA A:PRO195 4.7 34.1 1.0 CD2 A:TYR193 4.7 30.5 1.0 CA A:SER198 4.8 41.9 1.0 O A:HOH572 4.9 45.9 1.0 CA A:ASP200 4.9 33.4 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