Calcium in PDB 5fzp: Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis

The structure of Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis, PDB code: 5fzp was solved by S.Schmelz, D.Fiebig, J.Beck, H.L.Fuchsbauer, A.Scrima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.938 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.010, 101.130, 114.660, 90.00, 90.00, 90.00
R / Rfree (%)	15.93 / 19.13

The binding sites of Calcium atom in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis (pdb code 5fzp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis, PDB code: 5fzp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1350 b:13.0 occ:0.84 O A:LEU273 2.3 15.4 1.0 OE2 A:GLU272 2.3 14.5 1.0 O A:HOH2294 2.4 13.1 1.0 OD1 A:ASP267 2.4 14.5 1.0 O A:HOH2329 2.4 12.7 1.0 OD2 A:ASP267 2.5 13.3 1.0 O A:HOH2298 2.5 21.1 1.0 CG A:ASP267 2.8 10.4 1.0 C A:LEU273 3.5 13.6 1.0 CD A:GLU272 3.5 14.0 1.0 CA B:CA1351 3.7 13.1 0.8 O A:HOH2320 3.7 13.8 1.0 N A:LEU273 3.8 12.7 1.0 O A:HOH2293 3.8 23.1 1.0 CG A:GLU272 4.1 13.6 1.0 OE2 B:GLU272 4.2 14.0 1.0 CA A:LEU273 4.2 10.7 1.0 OE1 A:GLU247 4.2 15.5 1.0 NH1 A:ARG249 4.3 13.2 1.0 CB A:ASP267 4.3 11.8 1.0 OE1 A:GLU272 4.5 16.2 1.0 N A:THR274 4.5 11.0 1.0 OE1 B:GLU247 4.6 15.0 1.0 C A:GLU272 4.7 12.9 1.0 OE2 B:GLU247 4.7 14.4 1.0 CB A:LEU273 4.8 11.6 1.0 O A:HOH2328 4.8 14.0 1.0 CA A:THR274 4.8 10.9 1.0 CD B:GLU272 4.9 11.6 1.0 CA A:GLU272 4.9 11.0 1.0 CD A:ARG249 4.9 13.7 1.0 CG2 A:THR274 4.9 11.9 1.0 OE2 A:GLU247 4.9 17.6 1.0 CZ A:ARG249 5.0 15.8 1.0 CD A:GLU247 5.0 15.2 1.0

Calcium binding site 2 out of 4 in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1351 b:27.8 occ:0.54 O A:HOH2383 2.4 39.7 1.0 O A:HOH2391 2.4 44.7 1.0 O A:HOH2380 2.4 38.8 1.0 OD1 A:ASP322 2.5 19.6 1.0 O A:HOH2384 2.5 36.7 1.0 OE2 A:GLU343 2.5 28.9 1.0 OE1 A:GLU343 2.7 23.1 1.0 OD2 A:ASP322 2.8 23.3 1.0 CG A:ASP322 2.9 16.7 1.0 CD A:GLU343 2.9 25.1 1.0 O A:HOH2381 4.2 20.5 1.0 O A:HOH2358 4.2 34.8 1.0 O A:HOH2365 4.3 25.4 1.0 O A:VAL344 4.4 42.4 1.0 CB A:ASP322 4.4 13.7 1.0 CG A:GLU343 4.4 21.9 1.0 N A:ASP322 4.6 14.9 1.0 N A:VAL344 4.9 26.4 1.0 CB A:TYR296 4.9 21.8 1.0 O A:HOH2166 4.9 40.0 1.0 CA A:ASP322 5.0 13.6 1.0 O A:HOH2075 5.0 37.1 1.0

Calcium binding site 3 out of 4 in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1350 b:21.2 occ:0.75 O B:HOH2348 2.3 34.5 1.0 O B:HOH2340 2.4 36.3 1.0 O B:HOH2333 2.5 29.3 1.0 O B:HOH2339 2.5 28.8 1.0 OD1 B:ASP322 2.5 20.4 1.0 OD2 B:ASP322 2.6 21.9 1.0 OE2 B:GLU343 2.6 23.8 1.0 OE1 B:GLU343 2.6 26.2 1.0 CG B:ASP322 2.8 19.8 1.0 CD B:GLU343 3.0 24.9 1.0 O B:HOH2334 4.1 21.8 1.0 O B:VAL344 4.2 27.0 1.0 O B:HOH2310 4.2 25.7 1.0 O B:HOH2308 4.3 24.6 1.0 CB B:ASP322 4.3 16.6 1.0 CG B:GLU343 4.5 22.1 1.0 N B:ASP322 4.7 15.0 1.0 O B:HOH2335 4.8 38.5 1.0 N B:VAL344 4.9 20.8 1.0 O B:ALA320 5.0 18.4 1.0 CA B:ASP322 5.0 14.2 1.0 O B:HOH2062 5.0 36.7 1.0

Calcium binding site 4 out of 4 in the Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1351 b:13.1 occ:0.77 O B:LEU273 2.3 13.8 1.0 OE2 B:GLU272 2.3 14.0 1.0 O A:HOH2329 2.4 12.7 1.0 O A:HOH2294 2.5 13.1 1.0 OD2 B:ASP267 2.5 16.4 1.0 OD1 B:ASP267 2.5 12.1 1.0 O A:HOH2293 2.6 23.1 1.0 CG B:ASP267 2.8 11.9 1.0 C B:LEU273 3.5 11.2 1.0 CD B:GLU272 3.5 11.6 1.0 CA A:CA1350 3.7 13.0 0.8 O A:HOH2328 3.7 14.0 1.0 O A:HOH2298 3.8 21.1 1.0 N B:LEU273 3.8 12.6 1.0 OE2 A:GLU272 4.1 14.5 1.0 CG B:GLU272 4.2 13.0 1.0 OE1 B:GLU247 4.2 15.0 1.0 CA B:LEU273 4.2 10.6 1.0 NH1 B:ARG249 4.2 12.6 1.0 CB B:ASP267 4.4 12.5 1.0 OE1 B:GLU272 4.5 13.4 1.0 N B:THR274 4.6 11.0 1.0 OE1 A:GLU247 4.7 15.5 1.0 C B:GLU272 4.7 12.0 1.0 OE2 A:GLU247 4.7 17.6 1.0 O A:HOH2320 4.7 13.8 1.0 CD A:GLU272 4.8 14.0 1.0 CD B:ARG249 4.8 11.0 1.0 CA B:THR274 4.8 12.3 1.0 CB B:LEU273 4.9 14.4 1.0 CG2 B:THR274 4.9 15.1 1.0 CA B:GLU272 4.9 12.3 1.0 CZ B:ARG249 5.0 15.7 1.0 OE2 B:GLU247 5.0 14.4 1.0

D.Fiebig, S.Schmelz, S.Zindel, V.Ehret, J.Beck, A.Ebenig, M.Ehret, S.Froels, F.Pfeifer, H.Kolmar, H.L.Fuchsbauer, A.Scrima. Structure of the Dispase Autolysis Inducing Protein From Streptomyces Mobaraensis and Glutamine Cross-Linking Sites For Transglutaminase J.Biol.Chem. V. 291 20417 2016.
ISSN: ISSN 0021-9258
PubMed: 27493205
DOI: 10.1074/JBC.M116.731109