Calcium in PDB 2exh: Structure of the FAMILY43 Beta-Xylosidase From Geobacillus Stearothermophilus

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

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

Resolution Low / High (Å)	40.00 / 1.88
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.027, 140.027, 231.599, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.6

The binding sites of Calcium atom in the Structure of the FAMILY43 Beta-Xylosidase From Geobacillus Stearothermophilus (pdb code 2exh). 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 From Geobacillus Stearothermophilus, PDB code: 2exh:
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 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 From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:27.2 occ:1.00 O A:GLY362 2.2 24.0 1.0 OD2 A:ASP528 2.4 26.1 1.0 O A:ASP528 2.4 24.7 1.0 O A:ASP333 2.4 29.5 1.0 OD1 A:ASP333 2.5 32.9 1.0 O A:HOH2125 2.5 29.4 1.0 O A:HOH2139 2.5 36.6 1.0 C A:GLY362 3.3 24.7 1.0 CG A:ASP333 3.4 32.5 1.0 C A:ASP333 3.4 29.5 1.0 C A:ASP528 3.5 24.5 1.0 CG A:ASP528 3.5 26.2 1.0 CB A:ASP333 3.7 30.5 1.0 CA A:GLY362 3.8 25.1 1.0 CA A:ASP333 3.9 30.1 1.0 CA A:ASP528 4.0 24.6 1.0 OD1 A:ASP528 4.3 27.0 1.0 CB A:ASP528 4.4 24.7 1.0 N A:HIS363 4.5 23.9 1.0 OD2 A:ASP333 4.5 34.3 1.0 O A:HOH2202 4.5 42.4 1.0 N A:TYR529 4.6 24.7 1.0 N A:PHE334 4.6 29.7 1.0 O A:HOH2284 4.8 47.1 1.0 CB A:PHE334 4.8 29.0 1.0 CA A:HIS363 4.9 23.9 1.0 ND1 A:HIS363 4.9 24.7 1.0 OD1 A:ASP335 4.9 31.4 1.0 CE1 A:HIS363 5.0 27.4 1.0 CA A:TYR529 5.0 25.0 1.0

Calcium binding site 2 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase 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 From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:30.4 occ:1.00 O B:HOH2308 2.2 36.9 1.0 O B:GLY362 2.3 30.0 1.0 OD2 B:ASP528 2.3 27.7 1.0 O B:ASP528 2.4 23.1 1.0 O B:ASP333 2.4 26.7 1.0 O B:HOH2113 2.6 32.6 1.0 O B:HOH2162 2.6 38.0 1.0 C B:GLY362 3.4 29.9 1.0 C B:ASP333 3.4 27.0 1.0 C B:ASP528 3.4 24.3 1.0 CG B:ASP528 3.5 28.0 1.0 CA B:ASP333 3.8 27.2 1.0 CA B:GLY362 3.9 30.8 1.0 CB B:ASP333 3.9 27.5 1.0 CA B:ASP528 3.9 24.9 1.0 CB B:ASP528 4.3 25.3 1.0 OD1 B:ASP333 4.3 30.4 1.0 OD1 B:ASP528 4.4 29.9 1.0 N B:TYR529 4.5 23.6 1.0 N B:HIS363 4.5 29.4 1.0 N B:PHE334 4.6 27.3 1.0 CG B:ASP333 4.6 29.9 1.0 OD1 B:ASP335 4.6 31.9 1.0 CB B:PHE334 4.8 27.6 1.0 CB B:TYR529 4.9 23.9 1.0 CA B:TYR529 4.9 23.5 1.0 O B:HOH2398 4.9 43.5 1.0 ND1 B:HIS363 4.9 29.4 1.0 CA B:HIS363 5.0 28.6 1.0

Calcium binding site 3 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase 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 From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:61.7 occ:1.00 O C:ASP528 2.3 50.5 1.0 O C:ASP333 2.4 58.5 1.0 O C:HOH2113 2.4 41.0 1.0 O C:HOH2101 2.6 33.3 1.0 O C:GLY362 2.7 50.7 1.0 O C:HOH2143 3.1 49.0 1.0 C C:GLY362 3.3 50.6 1.0 C C:ASP528 3.3 50.5 1.0 C C:ASP333 3.4 58.8 1.0 CA C:GLY362 3.6 50.8 1.0 CA C:ASP333 3.7 59.0 1.0 CB C:ASP333 3.8 58.9 1.0 OD1 C:ASP528 3.8 52.7 1.0 O C:HOH2085 3.8 72.9 1.0 CG C:ASP528 3.9 51.8 1.0 CA C:ASP528 3.9 50.7 1.0 OD2 C:ASP528 4.1 52.8 1.0 OD2 C:ASP333 4.3 59.3 1.0 N C:HIS363 4.4 50.5 1.0 N C:TYR529 4.4 50.4 1.0 CB C:ASP528 4.4 50.8 1.0 CG C:ASP333 4.6 59.1 1.0 N C:PHE334 4.6 58.6 1.0 OD1 C:ASP335 4.8 58.0 1.0 CA C:TYR529 4.8 50.2 1.0 CB C:TYR529 4.8 50.5 1.0 CB C:PHE334 4.9 58.6 1.0 CA C:HIS363 4.9 50.3 1.0

Calcium binding site 4 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase 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 From Geobacillus Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2004 b:35.9 occ:1.00 OD1 D:ASP528 2.1 32.9 1.0 O D:ASP333 2.2 42.0 1.0 O D:GLY362 2.3 33.6 1.0 O D:ASP528 2.4 34.6 1.0 OD1 D:ASP333 2.8 41.9 1.0 O D:HOH2138 2.8 47.2 1.0 O D:HOH2393 3.2 41.6 1.0 C D:ASP333 3.3 42.1 1.0 CG D:ASP528 3.3 35.1 1.0 C D:GLY362 3.3 33.4 1.0 C D:ASP528 3.4 35.0 1.0 CG D:ASP333 3.7 42.3 1.0 CA D:GLY362 3.8 33.4 1.0 CA D:ASP333 3.8 42.2 1.0 CB D:ASP333 3.8 42.1 1.0 CA D:ASP528 3.9 34.9 1.0 OD2 D:ASP528 4.1 36.1 1.0 CB D:ASP528 4.2 34.8 1.0 O D:HOH2343 4.2 60.3 1.0 N D:PHE334 4.4 42.0 1.0 OD1 D:ASP335 4.4 43.0 1.0 O D:HOH2400 4.5 38.0 1.0 N D:TYR529 4.5 35.1 1.0 N D:HIS363 4.5 33.1 1.0 CB D:PHE334 4.6 41.6 1.0 CA D:PHE334 4.8 41.9 1.0 OD2 D:ASP333 4.9 41.3 1.0 CA D:TYR529 4.9 35.1 1.0 CB D:TYR529 4.9 35.6 1.0 C D:PHE334 4.9 42.2 1.0 CG D:ASP335 5.0 42.8 1.0 CA D:HIS363 5.0 33.0 1.0 OD2 D:ASP335 5.0 43.4 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