Calcium in PDB 2exi: Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus

All present enzymatic activity of Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus:
3.2.1.37;

The structure of Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus, PDB code: 2exi was solved by C.Brux, K.Niefind, D.Shallom-Shezifi, Y.Shoham, D.Schomburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.175, 140.175, 232.322, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 27.6

The binding sites of Calcium atom in the Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus (pdb code 2exi). 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 FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus, PDB code: 2exi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus


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 FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:25.0 occ:1.00 O A:GLY362 2.2 21.2 1.0 O A:HOH3128 2.4 24.6 1.0 OD2 A:ASP528 2.5 24.7 1.0 O A:ASP333 2.5 25.7 1.0 O A:ASP528 2.5 24.0 1.0 O A:HOH3086 2.6 23.5 1.0 OD1 A:ASP333 2.9 33.1 1.0 C A:GLY362 3.3 21.0 1.0 C A:ASP528 3.5 23.7 1.0 CG A:ASP528 3.5 24.8 1.0 C A:ASP333 3.5 26.1 1.0 CA A:GLY362 3.8 21.8 1.0 CG A:ASP333 3.8 30.4 1.0 CB A:ASP333 4.0 27.5 1.0 CA A:ASP528 4.0 23.6 1.0 CA A:ASP333 4.0 26.9 1.0 OD1 A:ASP528 4.3 26.1 1.0 CB A:ASP528 4.4 24.0 1.0 N A:HIS363 4.5 20.6 1.0 N A:TYR529 4.6 23.8 1.0 O A:HOH3132 4.7 35.6 1.0 N A:PHE334 4.7 25.7 1.0 OD1 A:ASP335 4.8 24.7 1.0 ND1 A:HIS363 4.8 22.9 1.0 CA A:HIS363 4.9 20.0 1.0 CB A:PHE334 4.9 25.1 1.0 O A:PHE334 4.9 26.1 1.0 CE1 A:HIS363 4.9 23.5 1.0 OD2 A:ASP333 5.0 34.3 1.0

Calcium binding site 2 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus


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 FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3002 b:27.9 occ:1.00 O B:HOH3504 2.2 29.4 1.0 O B:GLY362 2.3 24.4 1.0 OD2 B:ASP528 2.3 25.1 1.0 O B:ASP333 2.4 25.7 1.0 O B:ASP528 2.4 21.7 1.0 O B:HOH3065 2.7 23.8 1.0 O B:HOH3172 2.8 36.6 1.0 C B:GLY362 3.3 24.6 1.0 C B:ASP333 3.4 26.0 1.0 C B:ASP528 3.4 22.5 1.0 CG B:ASP528 3.5 25.5 1.0 CA B:GLY362 3.8 25.4 1.0 CA B:ASP333 3.8 26.1 1.0 CA B:ASP528 3.9 23.1 1.0 CB B:ASP333 4.0 26.6 1.0 CB B:ASP528 4.3 23.5 1.0 OD1 B:ASP333 4.4 28.7 1.0 O B:HOH3544 4.4 36.3 1.0 OD1 B:ASP528 4.4 26.2 1.0 N B:HIS363 4.5 24.2 1.0 N B:TYR529 4.5 21.9 1.0 N B:PHE334 4.5 26.1 1.0 CG B:ASP333 4.6 28.1 1.0 OD1 B:ASP335 4.7 28.1 1.0 CB B:PHE334 4.8 26.3 1.0 CB B:TYR529 4.9 21.5 1.0 ND1 B:HIS363 4.9 25.1 1.0 CA B:TYR529 4.9 21.4 1.0 CA B:HIS363 5.0 23.7 1.0 CE1 B:HIS363 5.0 24.0 1.0

Calcium binding site 3 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus


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 FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3003 b:57.1 occ:1.00 O C:ASP333 2.4 51.1 1.0 O C:GLY362 2.4 48.6 1.0 O C:ASP528 2.5 45.6 1.0 O C:HOH3137 2.5 31.5 1.0 O C:HOH3355 2.6 48.8 1.0 OD2 C:ASP528 2.8 50.1 1.0 OD2 C:ASP333 2.8 52.5 1.0 O C:HOH3069 3.0 33.4 1.0 C C:ASP333 3.3 51.7 1.0 C C:GLY362 3.4 48.5 1.0 C C:ASP528 3.4 45.8 1.0 CG C:ASP528 3.6 47.8 1.0 CA C:ASP333 3.7 52.0 1.0 CG C:ASP333 3.7 52.2 1.0 CB C:ASP333 3.8 52.0 1.0 CA C:GLY362 3.9 48.6 1.0 CA C:ASP528 3.9 46.0 1.0 OD1 C:ASP528 4.2 49.0 1.0 CB C:ASP528 4.4 46.3 1.0 N C:PHE334 4.5 51.5 1.0 N C:TYR529 4.6 45.8 1.0 N C:HIS363 4.6 48.2 1.0 OD1 C:ASP335 4.6 52.3 1.0 CB C:PHE334 4.9 51.5 1.0 OD1 C:ASP333 4.9 52.4 1.0 CB C:TYR529 4.9 45.8 1.0 CA C:TYR529 5.0 45.7 1.0

Calcium binding site 4 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus


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 FAMILY43 Beta-Xylosidase D15G Mutant From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3004 b:30.4 occ:1.00 OD1 D:ASP528 2.3 27.4 1.0 O D:ASP333 2.3 36.6 1.0 O D:GLY362 2.3 29.4 1.0 O D:ASP528 2.3 30.2 1.0 O D:HOH3482 2.6 41.9 1.0 O D:HOH3192 2.8 31.0 1.0 C D:GLY362 3.4 28.9 1.0 C D:ASP528 3.4 30.4 1.0 C D:ASP333 3.4 36.9 1.0 CG D:ASP528 3.4 29.9 1.0 CA D:GLY362 3.8 28.8 1.0 OD1 D:ASP333 3.9 37.8 1.0 CA D:ASP528 3.9 30.0 1.0 CA D:ASP333 3.9 37.0 1.0 CB D:ASP333 4.1 37.1 1.0 O D:HOH3370 4.2 41.9 1.0 CB D:ASP528 4.2 30.2 1.0 OD2 D:ASP528 4.3 31.8 1.0 OD1 D:ASP335 4.4 39.5 1.0 CG D:ASP333 4.5 37.6 1.0 N D:TYR529 4.5 30.5 1.0 N D:PHE334 4.5 36.6 1.0 N D:HIS363 4.5 28.9 1.0 O D:HOH3443 4.6 43.8 1.0 CB D:PHE334 4.7 36.3 1.0 O D:HOH3416 4.8 49.0 1.0 CB D:TYR529 4.8 30.6 1.0 CA D:TYR529 4.9 30.4 1.0 CA D:HIS363 4.9 29.0 1.0 CA D:PHE334 5.0 36.8 1.0

C.Brux, A.Ben-David, D.Shallom-Shezifi, M.Leon, K.Niefind, G.Shoham, Y.Shoham, D.Schomburg. The Structure of An Inverting GH43 Beta-Xylosidase From Geobacillus Stearothermophilus with Its Substrate Reveals the Role of the Three Catalytic Residues. J.Mol.Biol. V. 359 97 2006.
ISSN: ISSN 0022-2836
PubMed: 16631196
DOI: 10.1016/J.JMB.2006.03.005