Atomistry » Calcium » PDB 2eex-2f3z » 2exj
Atomistry »
  Calcium »
    PDB 2eex-2f3z »
      2exj »

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

Go back to Calcium Binding Sites List in 2exj
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

Go back to Calcium Binding Sites List in 2exj
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

Go back to Calcium Binding Sites List in 2exj
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

Go back to Calcium Binding Sites List in 2exj
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: Fri Jul 12 10:18:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy