Calcium in PDB 5wr2: Thermolysin, Sfx Liganded Form with Oil-Based Carrier

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

The structure of Thermolysin, Sfx Liganded Form with Oil-Based Carrier, PDB code: 5wr2 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 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.550, 93.550, 131.180, 90.00, 90.00, 120.00
R / Rfree (%)	13.2 / 16.9

The structure of Thermolysin, Sfx Liganded 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 Liganded Form with Oil-Based Carrier (pdb code 5wr2). 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 Liganded Form with Oil-Based Carrier, PDB code: 5wr2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin, Sfx Liganded 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 Liganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:33.0 occ:1.00 O A:GLN61 2.2 31.1 1.0 O A:HOH546 2.3 30.4 1.0 O A:HOH668 2.3 36.3 1.0 OD1 A:ASP57 2.4 32.0 1.0 OD1 A:ASP59 2.4 36.6 1.0 O A:HOH519 2.5 35.0 1.0 OD2 A:ASP57 2.6 31.7 1.0 CG A:ASP57 2.8 33.0 1.0 CG A:ASP59 3.3 41.2 1.0 C A:GLN61 3.4 32.9 1.0 OD2 A:ASP59 3.6 38.8 1.0 N A:GLN61 4.0 32.5 1.0 O A:HOH599 4.0 42.2 1.0 CA A:GLN61 4.1 36.3 1.0 N A:ASP59 4.3 33.6 1.0 O A:HOH630 4.3 37.7 1.0 CB A:ASP57 4.4 31.6 1.0 CB A:GLN61 4.4 33.4 1.0 N A:PHE62 4.5 31.4 1.0 OD2 A:ASP67 4.6 32.3 1.0 O A:HOH521 4.6 31.9 1.0 CB A:ASP59 4.6 37.7 1.0 CA A:PHE62 4.7 31.2 1.0 N A:ASN60 4.7 32.8 1.0 N A:ALA58 4.7 30.7 1.0 O A:HOH748 4.7 53.0 1.0 CA A:ASP59 4.8 34.0 1.0 C A:ASP59 4.9 39.1 1.0

Calcium binding site 2 out of 4 in the Thermolysin, Sfx Liganded 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 Liganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:30.8 occ:1.00 O A:GLU187 2.4 32.6 1.0 OE1 A:GLU177 2.4 31.5 1.0 OD2 A:ASP138 2.4 33.3 1.0 OE1 A:GLU190 2.5 31.8 1.0 O A:HOH597 2.5 31.1 1.0 OD1 A:ASP185 2.6 31.2 1.0 OE2 A:GLU190 2.6 30.9 1.0 OE2 A:GLU177 2.8 31.5 1.0 CD A:GLU190 2.9 32.5 1.0 CD A:GLU177 2.9 34.1 1.0 CG A:ASP138 3.4 32.3 1.0 C A:GLU187 3.4 32.8 1.0 CG A:ASP185 3.5 35.9 1.0 CA A:CA405 3.8 33.6 1.0 OD2 A:ASP185 3.8 34.5 1.0 CB A:ASP138 4.0 26.8 1.0 O A:ASP185 4.2 35.6 1.0 N A:GLU187 4.3 34.2 1.0 O A:HOH620 4.3 32.7 0.6 N A:ILE188 4.3 30.0 1.0 CA A:GLU187 4.3 36.9 1.0 CA A:ILE188 4.3 32.6 1.0 OD1 A:ASP138 4.4 34.2 1.0 CG A:GLU177 4.4 27.8 1.0 CG A:GLU190 4.4 33.0 1.0 N A:GLY189 4.4 34.0 1.0 O A:HOH549 4.5 34.5 1.0 CB A:GLU187 4.6 35.3 1.0 C A:ASP185 4.7 36.2 1.0 N A:ASP185 4.8 33.2 1.0 CB A:ASP185 4.8 34.8 1.0 C A:ILE188 4.8 36.7 1.0 O A:HOH516 4.9 34.2 1.0 CB A:GLU177 4.9 31.7 1.0 N A:GLU190 5.0 30.3 1.0

Calcium binding site 3 out of 4 in the Thermolysin, Sfx Liganded 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 Liganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:33.6 occ:1.00 OE2 A:GLU190 2.2 30.9 1.0 OD2 A:ASP185 2.3 34.5 1.0 O A:HOH545 2.4 36.6 1.0 O A:HOH516 2.4 34.2 1.0 OE2 A:GLU177 2.4 31.5 1.0 O A:ASN183 2.4 37.5 1.0 CD A:GLU177 3.2 34.1 1.0 CD A:GLU190 3.2 32.5 1.0 CG A:ASP185 3.2 35.9 1.0 C A:ASN183 3.5 35.6 1.0 OD1 A:ASP185 3.7 31.2 1.0 OE1 A:GLU177 3.8 31.5 1.0 CA A:CA404 3.8 30.8 1.0 CG A:GLU190 3.8 33.0 1.0 O A:LYS182 3.9 39.7 1.0 CB A:ASN183 4.1 42.5 1.0 OD1 A:ASP191 4.2 37.2 1.0 OE1 A:GLU190 4.2 31.8 1.0 OD2 A:ASP191 4.2 34.5 1.0 N A:ASP185 4.2 33.2 1.0 CG A:GLU177 4.2 27.8 1.0 CA A:PRO184 4.2 36.4 1.0 C A:PRO184 4.3 40.3 1.0 O A:HOH612 4.3 52.8 1.0 CB A:ASP185 4.4 34.8 1.0 N A:PRO184 4.4 37.6 1.0 O A:HOH620 4.4 32.7 0.6 CA A:ASN183 4.5 36.4 1.0 CG A:ASP191 4.5 35.1 1.0 O A:HOH757 4.7 59.4 1.0 O A:PRO184 4.9 38.4 1.0 C A:LYS182 4.9 42.7 1.0 CA A:ASP185 4.9 33.2 1.0

Calcium binding site 4 out of 4 in the Thermolysin, Sfx Liganded 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 Liganded Form with Oil-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:37.3 occ:1.00 O A:ILE197 2.3 47.5 1.0 OG1 A:THR194 2.3 35.3 1.0 O A:HOH641 2.4 46.8 1.0 O A:THR194 2.4 38.6 1.0 OD1 A:ASP200 2.4 37.6 1.0 O A:TYR193 2.4 32.4 1.0 O A:HOH504 2.5 37.6 1.0 C A:THR194 3.1 41.2 1.0 C A:TYR193 3.3 35.3 1.0 CB A:THR194 3.4 38.1 1.0 CG A:ASP200 3.4 35.0 1.0 C A:ILE197 3.5 47.8 1.0 CA A:THR194 3.6 38.5 1.0 OD2 A:ASP200 3.7 38.8 1.0 N A:THR194 3.8 33.6 1.0 CA A:ILE197 4.2 44.6 1.0 N A:PRO195 4.2 40.5 1.0 N A:ILE197 4.2 50.9 1.0 CB A:ILE197 4.2 47.5 1.0 O A:ASP200 4.3 37.7 1.0 CA A:TYR193 4.5 36.6 1.0 N A:SER198 4.5 48.4 1.0 O A:GLU190 4.6 36.0 1.0 O A:HOH656 4.6 45.3 1.0 CG2 A:THR194 4.7 36.5 1.0 CA A:PRO195 4.7 44.9 1.0 CD2 A:TYR193 4.7 37.2 1.0 CB A:TYR193 4.7 36.2 1.0 N A:ASP200 4.7 39.8 1.0 CA A:SER198 4.7 48.0 1.0 CB A:ASP200 4.7 36.2 1.0 C A:ASP200 4.8 37.5 1.0 O A:HOH624 4.8 55.3 1.0 CG2 A:ILE197 4.9 45.9 1.0 O A:HOH616 4.9 58.3 1.0 CA A:ASP200 5.0 39.4 1.0 C A:PRO195 5.0 49.6 1.0 C A:SER198 5.0 47.2 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