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Calcium in PDB 2exj: Structure of the FAMILY43 Beta-Xylosidase D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose

Enzymatic activity of Structure of the FAMILY43 Beta-Xylosidase D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose

All present enzymatic activity of Structure of the FAMILY43 Beta-Xylosidase D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose:
3.2.1.37;

Protein crystallography data

The structure of Structure of the FAMILY43 Beta-Xylosidase D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose, PDB code: 2exj 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) 30.00 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 140.383, 140.383, 232.907, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 28.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the FAMILY43 Beta-Xylosidase D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose (pdb code 2exj). 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 D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose, PDB code: 2exj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2exj

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Calcium binding site 1 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D128G Mutant 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 D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:29.0
occ:1.00
 O A:GLY362 2.2 25.6 1.0
OD2 A:ASP528 2.3 24.9 1.0
O A:ASP333 2.4 27.3 1.0
O A:HOH2100 2.4 27.4 1.0
O A:ASP528 2.5 26.6 1.0
O A:HOH2107 2.7 19.4 1.0
OD1 A:ASP333 3.0 39.7 1.0
C A:GLY362 3.4 24.6 1.0
CG A:ASP528 3.5 27.6 1.0
C A:ASP333 3.5 27.2 1.0
C A:ASP528 3.5 26.5 1.0
CG A:ASP333 3.9 34.4 1.0
CA A:GLY362 3.9 24.7 1.0
CB A:ASP333 3.9 29.9 1.0
CA A:ASP333 4.0 29.0 1.0
CA A:ASP528 4.0 26.0 1.0
OD1 A:ASP528 4.2 31.4 1.0
CB A:ASP528 4.4 26.3 1.0
N A:HIS363 4.5 24.3 1.0
O A:HOH2192 4.5 42.5 1.0
O A:HOH2304 4.6 40.6 1.0
N A:PHE334 4.6 27.0 1.0
N A:TYR529 4.7 25.9 1.0
CB A:PHE334 4.8 25.5 1.0
OD1 A:ASP335 4.9 27.1 1.0
ND1 A:HIS363 4.9 27.4 1.0
CA A:HIS363 4.9 24.1 1.0
CB A:TYR529 4.9 25.7 1.0
CE1 A:HIS363 5.0 27.0 1.0

Calcium binding site 2 out of 4 in 2exj

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Calcium binding site 2 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D128G Mutant 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 D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:29.0
occ:1.00
 O B:HOH2136 2.0 26.7 1.0
OD1 B:ASP528 2.2 28.2 1.0
O B:GLY362 2.3 29.0 1.0
O B:ASP333 2.4 29.8 1.0
O B:ASP528 2.4 22.5 1.0
O B:HOH2096 2.6 25.7 1.0
O B:HOH2127 2.8 22.7 1.0
C B:GLY362 3.4 29.5 1.0
C B:ASP333 3.4 30.0 1.0
CG B:ASP528 3.4 28.9 1.0
C B:ASP528 3.4 24.1 1.0
CA B:ASP333 3.8 30.2 1.0
CA B:GLY362 3.8 30.2 1.0
CB B:ASP333 3.9 31.1 1.0
CA B:ASP528 3.9 24.6 1.0
CB B:ASP528 4.3 25.5 1.0
OD1 B:ASP333 4.3 32.8 1.0
OD2 B:ASP528 4.3 30.2 1.0
O B:HOH2437 4.4 32.2 1.0
N B:HIS363 4.5 28.8 1.0
CG B:ASP333 4.5 33.5 1.0
N B:PHE334 4.6 30.0 1.0
OD1 B:ASP335 4.6 32.7 1.0
N B:TYR529 4.6 23.5 1.0
ND1 B:HIS363 4.7 31.3 1.0
O B:HOH2386 4.7 37.8 1.0
CB B:PHE334 4.8 30.1 1.0
CE1 B:HIS363 4.9 30.6 1.0
CB B:TYR529 4.9 24.3 1.0
CA B:HIS363 4.9 28.2 1.0
CA B:TYR529 4.9 23.3 1.0

Calcium binding site 3 out of 4 in 2exj

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Calcium binding site 3 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D128G Mutant 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 D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:51.0
occ:1.00
 O C:ASP333 2.1 61.0 1.0
O C:GLY362 2.3 57.8 1.0
O C:ASP528 2.5 53.8 1.0
OD2 C:ASP333 2.5 62.8 1.0
OD2 C:ASP528 2.6 59.0 1.0
O C:HOH2174 2.7 42.3 1.0
O C:HOH2048 3.1 30.6 1.0
C C:ASP333 3.2 62.0 1.0
C C:GLY362 3.2 57.6 1.0
C C:ASP528 3.4 54.3 1.0
CG C:ASP333 3.6 62.8 1.0
CG C:ASP528 3.6 56.6 1.0
CA C:GLY362 3.7 57.6 1.0
CA C:ASP333 3.7 62.6 1.0
CA C:ASP528 3.8 54.5 1.0
CB C:ASP333 3.9 62.7 1.0
CB C:ASP528 4.3 54.9 1.0
N C:PHE334 4.3 61.6 1.0
OD1 C:ASP335 4.4 61.6 1.0
N C:HIS363 4.4 57.4 1.0
OD1 C:ASP528 4.4 56.1 1.0
CB C:PHE334 4.5 61.6 1.0
N C:TYR529 4.6 54.5 1.0
ND1 C:HIS363 4.7 60.1 1.0
OD1 C:ASP333 4.7 62.5 1.0
O C:HOH2205 4.7 43.2 1.0
CA C:PHE334 4.8 61.9 1.0
CA C:HIS363 4.8 57.3 1.0
CE1 C:HIS363 4.8 60.4 1.0
C C:PHE334 5.0 62.3 1.0

Calcium binding site 4 out of 4 in 2exj

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Calcium binding site 4 out of 4 in the Structure of the FAMILY43 Beta-Xylosidase D128G Mutant 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 D128G Mutant From Geobacillus Stearothermophilus in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2004

b:37.4
occ:1.00
 OD1 D:ASP528 2.1 28.5 1.0
O D:ASP333 2.3 42.7 1.0
O D:ASP528 2.3 37.0 1.0
O D:GLY362 2.3 36.6 1.0
O D:HOH2092 3.0 44.1 1.0
O D:HOH2261 3.1 47.9 1.0
OD1 D:ASP333 3.3 44.5 1.0
CG D:ASP528 3.3 34.4 1.0
C D:ASP528 3.3 36.2 1.0
C D:ASP333 3.3 43.3 1.0
C D:GLY362 3.4 35.9 1.0
CA D:ASP528 3.8 35.2 1.0
CA D:GLY362 3.8 35.3 1.0
CA D:ASP333 3.9 43.9 1.0
CB D:ASP333 4.0 44.1 1.0
CB D:ASP528 4.1 35.1 1.0
CG D:ASP333 4.1 45.8 1.0
OD2 D:ASP528 4.2 34.8 1.0
N D:TYR529 4.5 36.9 1.0
N D:PHE334 4.5 42.7 1.0
N D:HIS363 4.5 36.1 1.0
OD1 D:ASP335 4.6 43.7 1.0
CB D:PHE334 4.7 41.7 1.0
CB D:TYR529 4.8 37.8 1.0
CA D:HIS363 4.9 36.5 1.0
CA D:TYR529 4.9 37.2 1.0
CA D:PHE334 5.0 42.2 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 05:25:26 2025

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