Calcium in PDB 6zhj: 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus

All present enzymatic activity of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus:
3.4.24.27;

The structure of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus (pdb code 6zhj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus, PDB code: 6zhj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:23.3 occ:1.00 OE1 A:GLU177 2.4 36.5 1.0 OD2 A:ASP138 2.6 39.0 1.0 OE2 A:GLU190 2.6 34.6 1.0 O A:GLU187 2.6 40.2 1.0 OE1 A:GLU190 3.0 32.0 1.0 CD A:GLU190 3.1 33.7 1.0 OD1 A:ASP185 3.1 45.4 1.0 CD A:GLU177 3.1 37.9 1.0 OE2 A:GLU177 3.2 37.0 1.0 CG A:ASP138 3.3 41.0 1.0 C A:GLU187 3.6 45.5 1.0 CB A:ASP138 3.6 39.1 1.0 CG A:ASP185 3.8 47.0 1.0 N A:GLY189 3.9 48.9 1.0 OD2 A:ASP185 4.1 49.6 1.0 O A:ASP185 4.2 34.5 1.0 N A:ILE188 4.3 50.6 1.0 CA A:CA502 4.3 31.9 1.0 OD1 A:ASP138 4.3 41.3 1.0 CA A:ILE188 4.4 54.7 1.0 CA A:GLU187 4.5 47.4 1.0 OD1 A:ASP191 4.5 36.2 1.0 CG A:GLU177 4.5 36.9 1.0 N A:GLU187 4.6 42.7 1.0 CG A:GLU190 4.6 35.2 1.0 C A:ILE188 4.7 54.0 1.0 CB A:GLU187 4.7 53.7 1.0 CA A:GLY189 4.7 43.8 1.0 N A:GLU190 4.8 37.2 1.0 CA A:ASP138 4.9 33.0 1.0 C A:ASP185 4.9 36.0 1.0

Calcium binding site 2 out of 4 in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:31.9 occ:1.00 O A:ASN183 2.5 41.7 1.0 OE2 A:GLU177 2.6 37.0 1.0 OE2 A:GLU190 3.1 34.6 1.0 OD1 A:ASP185 3.3 45.4 1.0 CB A:ASN183 3.6 43.7 1.0 C A:ASN183 3.6 42.6 1.0 O A:LYS182 3.8 47.4 1.0 OD2 A:ASP185 3.8 49.6 1.0 CD A:GLU177 3.8 37.9 1.0 CG A:ASP185 3.9 47.0 1.0 OD1 A:ASP191 3.9 36.2 1.0 CD A:GLU190 4.0 33.7 1.0 CA A:ASN183 4.1 44.0 1.0 CA A:CA501 4.3 23.3 1.0 CG A:GLU190 4.4 35.2 1.0 OE1 A:GLU177 4.5 36.5 1.0 CG A:ASP191 4.6 34.6 1.0 CB A:ASP191 4.6 33.3 1.0 C A:LYS182 4.6 49.2 1.0 N A:PRO184 4.8 40.4 1.0 N A:ASN183 4.8 46.5 1.0 CG A:GLU177 4.9 36.9 1.0 CG A:ASN183 4.9 43.7 1.0 OE1 A:GLU190 5.0 32.0 1.0 OD2 A:ASP138 5.0 39.0 1.0

Calcium binding site 3 out of 4 in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:16.9 occ:1.00 OD1 A:ASP57 2.5 27.0 1.0 O A:GLN61 2.5 27.7 1.0 OD1 A:ASP59 2.6 26.6 1.0 OD2 A:ASP57 2.9 28.4 1.0 CG A:ASP57 3.0 28.5 1.0 CG A:ASP59 3.5 26.9 1.0 C A:GLN61 3.6 27.5 1.0 N A:GLN61 4.0 25.6 1.0 OD2 A:ASP59 4.1 23.8 1.0 N A:ASP59 4.2 28.0 1.0 CA A:GLN61 4.3 26.3 1.0 CB A:ASP57 4.5 28.2 1.0 CB A:ASP59 4.5 28.1 1.0 N A:ALA58 4.6 31.7 1.0 CB A:GLN61 4.6 27.8 1.0 N A:PHE62 4.7 29.1 1.0 N A:ASN60 4.7 23.0 1.0 CA A:ASP59 4.7 27.6 1.0 C A:ASP59 4.9 25.2 1.0 CA A:PHE62 4.9 30.0 1.0 OD2 A:ASP67 5.0 28.6 1.0

Calcium binding site 4 out of 4 in the 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 3D Electron Diffraction Structure of Thermolysin From Bacillus Thermoproteolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:29.5 occ:1.00 O A:TYR193 2.5 37.0 1.0 O A:THR194 2.5 49.1 1.0 O A:ILE197 2.7 40.9 1.0 OD1 A:ASP200 2.8 45.7 1.0 OG1 A:THR194 2.9 43.2 1.0 O A:GLU190 3.2 37.0 1.0 C A:ILE197 3.6 42.6 1.0 C A:TYR193 3.6 38.6 1.0 C A:THR194 3.6 45.9 1.0 CA A:SER198 3.9 41.2 1.0 CG A:ASP200 4.0 45.1 1.0 N A:SER198 4.0 41.4 1.0 CB A:THR194 4.1 45.3 1.0 O A:ASP200 4.2 42.5 1.0 CA A:THR194 4.2 42.6 1.0 N A:GLY199 4.2 39.2 1.0 C A:GLU190 4.2 36.3 1.0 N A:THR194 4.3 40.2 1.0 N A:ASP200 4.4 40.2 1.0 C A:SER198 4.4 39.9 1.0 C A:ASP200 4.5 42.6 1.0 CA A:GLU190 4.6 36.5 1.0 CB A:ASP200 4.7 47.1 1.0 N A:PRO195 4.7 49.5 1.0 CA A:TYR193 4.7 38.6 1.0 CA A:ILE197 4.7 45.6 1.0 N A:TYR193 4.7 37.8 1.0 CA A:ASP200 4.8 44.5 1.0 N A:ILE197 4.8 43.4 1.0 CA A:PRO195 4.9 49.9 1.0 OD2 A:ASP200 4.9 43.0 1.0

T.B.Blum, D.Housset, M.T.B.Clabbers, E.Van Genderen, M.Bacia-Verloop, U.Zander, A.A.Mccarthy, G.Schoehn, W.L.Ling, J.P.Abrahams. Statistically Correcting Dynamical Electron Scattering Improves the Refinement of Protein Nanocrystals, Including Charge Refinement of Coordinated Metals. Acta Crystallogr D Struct V. 77 75 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 33404527
DOI: 10.1107/S2059798320014540