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

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

Enzymatic activity of 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;

Protein crystallography data

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

Calcium Binding Sites:

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 2exi

Go back to Calcium Binding Sites List in 2exi
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 2exi

Go back to Calcium Binding Sites List in 2exi
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 2exi

Go back to Calcium Binding Sites List in 2exi
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 2exi

Go back to Calcium Binding Sites List in 2exi
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

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 05:25:24 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy