Calcium in PDB 5wr3: Thermolysin, Sfx Liganded Form with Water-Based Carrier

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

The structure of Thermolysin, Sfx Liganded Form with Water-Based Carrier, PDB code: 5wr3 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)	44.10 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.590, 93.590, 131.220, 90.00, 90.00, 120.00
R / Rfree (%)	12.6 / 16

The structure of Thermolysin, Sfx Liganded Form with Water-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 Water-Based Carrier (pdb code 5wr3). 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 Water-Based Carrier, PDB code: 5wr3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thermolysin, Sfx Liganded Form with Water-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 Water-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:27.6 occ:1.00 O A:GLN61 2.3 25.1 1.0 O A:HOH692 2.4 27.0 1.0 O A:HOH546 2.4 23.9 1.0 O A:HOH533 2.4 29.3 1.0 OD1 A:ASP59 2.4 28.8 1.0 OD1 A:ASP57 2.4 27.3 1.0 OD2 A:ASP57 2.6 27.2 1.0 CG A:ASP57 2.8 25.6 1.0 CG A:ASP59 3.4 31.4 1.0 C A:GLN61 3.4 26.7 1.0 OD2 A:ASP59 3.7 29.2 1.0 O A:HOH578 3.9 38.6 1.0 N A:GLN61 4.0 26.4 1.0 CA A:GLN61 4.2 28.0 1.0 CB A:ASP57 4.3 23.3 1.0 N A:ASP59 4.4 25.1 1.0 CB A:GLN61 4.4 27.3 1.0 O A:HOH661 4.4 32.4 1.0 N A:PHE62 4.5 25.2 1.0 OD2 A:ASP67 4.6 26.1 1.0 CB A:ASP59 4.6 27.4 1.0 O A:HOH528 4.7 25.4 1.0 CA A:PHE62 4.7 25.9 1.0 N A:ASN60 4.7 27.6 1.0 N A:ALA58 4.8 24.5 1.0 CA A:ASP59 4.8 26.4 1.0 O A:HOH766 4.9 50.3 1.0 C A:ASP59 4.9 30.4 1.0

Calcium binding site 2 out of 4 in the Thermolysin, Sfx Liganded Form with Water-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 Water-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:29.1 occ:1.00 O A:GLU187 2.3 28.3 1.0 O A:HOH611 2.5 25.7 1.0 OD2 A:ASP138 2.5 26.5 1.0 OE2 A:GLU190 2.5 25.8 1.0 OE1 A:GLU190 2.5 30.7 1.0 OE1 A:GLU177 2.6 27.9 1.0 OD1 A:ASP185 2.6 28.1 1.0 OE2 A:GLU177 2.7 29.3 1.0 CD A:GLU190 2.9 30.4 1.0 CD A:GLU177 3.0 30.4 1.0 C A:GLU187 3.4 31.2 1.0 CG A:ASP138 3.5 25.4 1.0 CG A:ASP185 3.5 33.8 1.0 CA A:CA405 3.8 32.7 0.7 OD2 A:ASP185 3.8 35.1 1.0 CB A:ASP138 4.0 18.9 1.0 O A:HOH505 4.2 32.0 0.6 O A:ASP185 4.2 32.8 1.0 N A:GLU187 4.3 28.9 1.0 N A:ILE188 4.3 27.7 1.0 CA A:ILE188 4.3 25.6 1.0 CA A:GLU187 4.3 32.4 1.0 CG A:GLU190 4.4 27.1 1.0 OD1 A:ASP138 4.4 27.4 1.0 CG A:GLU177 4.4 23.3 1.0 N A:GLY189 4.5 26.5 1.0 C A:ASP185 4.7 30.8 1.0 O A:HOH567 4.7 29.2 1.0 CB A:GLU187 4.7 31.8 1.0 N A:ASP185 4.8 30.8 1.0 CB A:ASP185 4.8 31.4 1.0 C A:ILE188 4.8 27.5 1.0 N A:GLU190 4.9 25.7 1.0 CB A:GLU177 4.9 24.7 1.0 O A:HOH553 5.0 38.7 1.0

Calcium binding site 3 out of 4 in the Thermolysin, Sfx Liganded Form with Water-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 Water-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:32.7 occ:0.72 OE2 A:GLU190 2.3 25.8 1.0 O A:HOH553 2.4 38.7 1.0 O A:HOH576 2.4 40.8 1.0 OD2 A:ASP185 2.4 35.1 1.0 OE2 A:GLU177 2.6 29.3 1.0 O A:ASN183 2.6 36.8 1.0 CD A:GLU177 3.2 30.4 1.0 CD A:GLU190 3.2 30.4 1.0 CG A:ASP185 3.3 33.8 1.0 OE1 A:GLU177 3.6 27.9 1.0 C A:ASN183 3.7 34.4 1.0 OD1 A:ASP185 3.7 28.1 1.0 CA A:CA404 3.8 29.1 1.0 CG A:GLU190 3.8 27.1 1.0 O A:LYS182 3.9 45.8 1.0 N A:ASP185 4.2 30.8 1.0 CA A:PRO184 4.2 36.6 1.0 OE1 A:GLU190 4.2 30.7 1.0 OD1 A:ASP191 4.3 36.1 1.0 CG A:GLU177 4.3 23.3 1.0 CB A:ASN183 4.3 42.9 1.0 C A:PRO184 4.3 36.4 1.0 OD2 A:ASP191 4.3 37.8 1.0 O A:HOH505 4.4 32.0 0.6 CB A:ASP185 4.4 31.4 1.0 N A:PRO184 4.5 33.5 1.0 CG A:ASP191 4.6 31.0 1.0 CA A:ASN183 4.6 36.0 1.0 CA A:ASP185 4.9 25.9 1.0 C A:LYS182 5.0 46.2 1.0

Calcium binding site 4 out of 4 in the Thermolysin, Sfx Liganded Form with Water-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 Water-Based Carrier within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:31.6 occ:1.00 OG1 A:THR194 2.3 31.8 1.0 O A:HOH671 2.3 39.3 1.0 OD1 A:ASP200 2.3 30.7 1.0 O A:ILE197 2.4 40.5 1.0 O A:THR194 2.4 32.9 1.0 O A:TYR193 2.4 26.6 1.0 O A:HOH527 2.4 28.6 1.0 C A:THR194 3.2 36.8 1.0 C A:TYR193 3.3 28.9 1.0 CG A:ASP200 3.4 32.7 1.0 CB A:THR194 3.4 33.5 1.0 C A:ILE197 3.5 43.8 1.0 CA A:THR194 3.6 32.1 1.0 OD2 A:ASP200 3.7 29.6 1.0 N A:THR194 3.9 30.0 1.0 N A:PRO195 4.2 34.7 1.0 CA A:ILE197 4.3 40.3 1.0 N A:ILE197 4.3 47.8 1.0 CB A:ILE197 4.4 43.9 1.0 O A:ASP200 4.4 32.7 1.0 O A:HOH659 4.5 41.7 1.0 CA A:TYR193 4.5 30.2 1.0 O A:GLU190 4.5 31.1 1.0 N A:SER198 4.6 41.1 1.0 CA A:PRO195 4.7 35.0 1.0 CG2 A:THR194 4.7 32.7 1.0 N A:ASP200 4.7 34.2 1.0 CB A:TYR193 4.7 30.8 1.0 CB A:ASP200 4.7 30.5 1.0 CA A:SER198 4.7 40.0 1.0 C A:ASP200 4.7 32.1 1.0 CD2 A:TYR193 4.8 32.8 1.0 O A:HOH602 4.9 53.7 1.0 CA A:ASP200 5.0 33.3 1.0 C A:SER198 5.0 40.6 1.0 C A:PRO195 5.0 45.2 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