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Calcium in PDB 2exk: Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose

Enzymatic activity of Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose

All present enzymatic activity of Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose:
3.2.1.37;

Protein crystallography data

The structure of Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose, PDB code: 2exk 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) 2.23 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 139.870, 139.870, 232.025, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose (pdb code 2exk). 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 E187G From Geobacillus Stearothermophilus in Complex with Xylobiose, PDB code: 2exk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2exk

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Calcium binding site 1 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose


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 E187G From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:36.7
occ:1.00
 O A:GLY362 2.2 34.7 1.0
O A:HOH2054 2.4 41.9 1.0
OD2 A:ASP528 2.4 35.2 1.0
O A:ASP528 2.4 34.2 1.0
O A:ASP333 2.5 37.1 1.0
O A:HOH2062 2.7 33.9 1.0
OD1 A:ASP333 2.8 44.2 1.0
C A:GLY362 3.3 34.8 1.0
C A:ASP333 3.5 37.2 1.0
C A:ASP528 3.5 34.6 1.0
CG A:ASP528 3.5 35.0 1.0
CG A:ASP333 3.7 42.1 1.0
CA A:GLY362 3.9 35.1 1.0
CB A:ASP333 3.9 38.3 1.0
CA A:ASP333 3.9 37.8 1.0
CA A:ASP528 4.0 34.5 1.0
OD1 A:ASP528 4.3 36.7 1.0
O A:HOH2320 4.4 51.0 1.0
CB A:ASP528 4.4 34.8 1.0
N A:HIS363 4.5 34.2 1.0
N A:TYR529 4.6 34.8 1.0
N A:PHE334 4.6 37.4 1.0
ND1 A:HIS363 4.8 34.3 1.0
O A:HOH2294 4.8 48.5 1.0
CA A:HIS363 4.8 33.5 1.0
CB A:PHE334 4.9 37.2 1.0
OD2 A:ASP333 4.9 46.2 1.0
CE1 A:HIS363 4.9 34.8 1.0
CA A:TYR529 5.0 34.8 1.0
OD1 A:ASP335 5.0 41.7 1.0
O A:PHE334 5.0 38.4 1.0
CB A:TYR529 5.0 35.2 1.0

Calcium binding site 2 out of 4 in 2exk

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Calcium binding site 2 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose


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 E187G From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:38.6
occ:1.00
 O B:GLY362 2.2 36.5 1.0
OD2 B:ASP528 2.2 38.1 1.0
O B:HOH2255 2.2 47.4 1.0
O B:ASP528 2.4 36.6 1.0
O B:ASP333 2.4 40.4 1.0
O B:HOH2100 2.6 50.9 1.0
O B:HOH2262 2.6 39.6 1.0
C B:GLY362 3.3 37.4 1.0
CG B:ASP528 3.4 37.9 1.0
C B:ASP528 3.4 36.7 1.0
C B:ASP333 3.4 40.2 1.0
CA B:GLY362 3.8 37.8 1.0
CA B:ASP333 3.9 40.4 1.0
CA B:ASP528 3.9 36.7 1.0
CB B:ASP333 4.0 40.7 1.0
OD1 B:ASP333 4.1 43.6 1.0
OD1 B:ASP528 4.2 40.0 1.0
CB B:ASP528 4.2 36.7 1.0
OD1 B:ASP335 4.5 43.3 1.0
N B:HIS363 4.5 36.8 1.0
CG B:ASP333 4.5 43.0 1.0
N B:TYR529 4.5 37.0 1.0
N B:PHE334 4.6 40.1 1.0
CB B:PHE334 4.8 39.5 1.0
CB B:TYR529 4.8 36.9 1.0
ND1 B:HIS363 4.8 35.6 1.0
CA B:HIS363 4.9 36.4 1.0
CA B:TYR529 4.9 36.9 1.0
CE1 B:HIS363 5.0 34.7 1.0

Calcium binding site 3 out of 4 in 2exk

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Calcium binding site 3 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose


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 E187G From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:75.3
occ:1.00
 O C:GLY362 2.3 52.9 1.0
O C:ASP528 2.5 50.4 1.0
O C:ASP333 2.6 60.0 1.0
O C:HOH2080 2.8 61.8 1.0
OD2 C:ASP333 2.9 60.9 1.0
OD2 C:ASP528 3.1 50.4 1.0
O C:HOH2100 3.2 47.5 1.0
C C:ASP528 3.4 50.5 1.0
C C:GLY362 3.4 52.8 1.0
CG C:ASP528 3.5 50.4 1.0
C C:ASP333 3.5 60.4 1.0
CG C:ASP333 3.7 60.6 1.0
CB C:ASP333 3.8 60.5 1.0
CA C:ASP333 3.8 60.5 1.0
OD1 C:ASP528 3.8 52.0 1.0
CA C:ASP528 3.9 50.6 1.0
CA C:GLY362 3.9 53.1 1.0
CB C:ASP528 4.2 50.6 1.0
N C:TYR529 4.4 50.4 1.0
N C:HIS363 4.5 52.5 1.0
OD1 C:ASP335 4.6 60.0 1.0
N C:PHE334 4.7 60.3 1.0
CB C:TYR529 4.9 50.3 1.0
CA C:TYR529 4.9 50.5 1.0
CA C:HIS363 4.9 52.1 1.0
CD2 C:HIS363 4.9 52.8 1.0
NE2 C:HIS363 4.9 53.1 1.0
OD1 C:ASP333 4.9 60.8 1.0
CG C:HIS363 5.0 52.5 1.0
CE1 C:HIS363 5.0 53.2 1.0

Calcium binding site 4 out of 4 in 2exk

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Calcium binding site 4 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase E187G From Geobacillus Stearothermophilus in Complex with Xylobiose


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 E187G From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2004

b:56.8
occ:1.00
 O D:GLY362 2.2 39.0 1.0
OD1 D:ASP528 2.3 39.6 1.0
O D:ASP333 2.4 48.2 1.0
O D:HOH2111 2.5 52.1 1.0
O D:ASP528 2.5 42.6 1.0
OD1 D:ASP333 2.9 50.0 1.0
CG D:ASP528 3.3 41.3 1.0
C D:GLY362 3.3 38.8 1.0
C D:ASP333 3.4 48.3 1.0
C D:ASP528 3.5 42.3 1.0
O D:HOH2263 3.6 51.6 1.0
CG D:ASP333 3.8 49.6 1.0
CA D:ASP333 3.8 48.4 1.0
CB D:ASP333 3.8 48.6 1.0
CA D:GLY362 3.9 38.7 1.0
CA D:ASP528 4.0 41.9 1.0
OD2 D:ASP528 4.1 41.5 1.0
CB D:ASP528 4.2 41.9 1.0
N D:HIS363 4.5 39.1 1.0
N D:PHE334 4.5 48.4 1.0
OD1 D:ASP335 4.5 49.4 1.0
N D:TYR529 4.6 42.6 1.0
CB D:PHE334 4.7 48.2 1.0
CA D:HIS363 4.9 38.9 1.0
CD2 D:HIS363 4.9 38.8 1.0
NE2 D:HIS363 4.9 39.0 1.0
CA D:TYR529 4.9 42.8 1.0
CB D:TYR529 5.0 42.8 1.0
CA D:PHE334 5.0 48.5 1.0
CG D:HIS363 5.0 39.2 1.0

Reference:

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
Page generated: Tue Jul 8 05:25:33 2025

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