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Calcium in PDB 2bs9: Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus

Enzymatic activity of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus

All present enzymatic activity of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus:
3.2.1.37;

Protein crystallography data

The structure of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus, PDB code: 2bs9 was solved by M.Czjzek, T.Bravman, B.Henrissat, Y.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.2
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.668, 165.744, 311.004, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus (pdb code 2bs9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus, PDB code: 2bs9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2bs9

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Calcium binding site 1 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 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 Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:23.5
occ:1.00
 N A:GLU323 3.2 11.7 1.0
O A:HOH2123 3.2 14.5 1.0
NE1 A:TRP117 3.3 11.1 1.0
N A:ARG26 3.4 11.1 1.0
N A:GLU324 3.6 12.6 1.0
CD1 A:LEU29 3.8 10.4 1.0
CG A:ARG26 3.9 13.4 1.0
CA A:GLU323 4.0 12.0 1.0
CB A:ARG26 4.0 11.8 1.0
CA A:GLY25 4.0 11.1 1.0
CG A:GLU324 4.0 11.6 1.0
C A:GLU323 4.0 12.5 1.0
CD1 A:TRP117 4.0 12.1 1.0
CA A:PHE322 4.1 11.8 1.0
CE2 A:TRP117 4.1 11.7 1.0
C A:PHE322 4.1 11.9 1.0
CD1 A:PHE322 4.1 12.2 1.0
CG A:PHE322 4.2 11.4 1.0
C A:GLY25 4.2 11.0 1.0
CE1 A:PHE322 4.3 12.6 1.0
CA A:ARG26 4.3 11.7 1.0
NH1 A:ARG26 4.3 14.8 1.0
CB A:GLU323 4.3 12.1 1.0
CD2 A:PHE322 4.4 12.8 1.0
CA A:GLU324 4.4 12.8 1.0
CZ A:PHE322 4.5 12.6 1.0
CZ2 A:TRP117 4.5 11.2 1.0
CE2 A:PHE322 4.5 14.0 1.0
CD A:ARG26 4.6 13.3 1.0
CB A:GLU324 4.7 12.9 1.0
CB A:PHE322 4.8 11.5 1.0
O A:GLU323 4.9 12.6 1.0
O A:HOH2010 4.9 15.6 1.0
CG A:LEU29 5.0 12.1 1.0

Calcium binding site 2 out of 7 in 2bs9

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Calcium binding site 2 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 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 Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1503

b:24.1
occ:1.00
 N C:GLU323 3.2 12.6 1.0
NE1 C:TRP117 3.2 12.1 1.0
O C:HOH2119 3.3 15.0 1.0
N C:ARG26 3.4 11.8 1.0
N C:GLU324 3.6 13.5 1.0
CD1 C:LEU29 3.9 10.3 1.0
CA C:GLU323 3.9 12.2 1.0
C C:GLU323 4.0 12.9 1.0
CD1 C:TRP117 4.0 12.8 1.0
CG C:GLU324 4.0 12.7 1.0
CB C:ARG26 4.0 11.6 1.0
CA C:GLY25 4.1 11.8 1.0
CE2 C:TRP117 4.1 12.5 1.0
CG C:ARG26 4.2 10.1 1.0
CD1 C:PHE322 4.2 13.9 1.0
C C:PHE322 4.2 12.5 1.0
CG C:PHE322 4.2 14.0 1.0
CA C:PHE322 4.2 12.9 1.0
CB C:GLU323 4.2 12.0 1.0
C C:GLY25 4.3 11.9 1.0
NH1 C:ARG26 4.3 9.7 1.0
CD C:ARG26 4.3 10.5 1.0
CE1 C:PHE322 4.3 15.3 1.0
CA C:ARG26 4.3 11.6 1.0
CD2 C:PHE322 4.4 14.1 1.0
CA C:GLU324 4.4 13.1 1.0
CZ C:PHE322 4.5 15.3 1.0
CZ2 C:TRP117 4.5 10.1 1.0
CE2 C:PHE322 4.6 15.1 1.0
CB C:GLU324 4.7 13.5 1.0
O C:GLU323 4.8 13.4 1.0
CB C:PHE322 4.8 13.4 1.0
CG C:LEU29 4.9 11.3 1.0
O C:HOH2011 4.9 12.0 1.0
CD C:GLU324 5.0 13.4 1.0
OE2 C:GLU324 5.0 14.7 1.0

Calcium binding site 3 out of 7 in 2bs9

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Calcium binding site 3 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 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 Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1503

b:24.7
occ:1.00
 O D:HOH2119 3.0 12.6 1.0
NE1 D:TRP117 3.2 12.7 1.0
N D:ARG26 3.3 13.4 1.0
N D:GLU323 3.3 13.7 1.0
CD1 D:LEU29 3.7 11.4 1.0
CG D:GLU324 3.7 13.7 1.0
CG D:ARG26 3.8 12.5 1.0
CB D:ARG26 3.8 12.8 1.0
N D:GLU324 3.8 13.8 1.0
CA D:GLY25 4.0 12.9 1.0
CD1 D:TRP117 4.0 13.6 1.0
CE2 D:TRP117 4.1 11.2 1.0
C D:GLY25 4.1 13.4 1.0
CD1 D:PHE322 4.1 11.5 1.0
CA D:GLU323 4.1 13.7 1.0
CA D:PHE322 4.1 13.3 1.0
CA D:ARG26 4.2 12.9 1.0
C D:GLU323 4.2 13.8 1.0
C D:PHE322 4.2 13.8 1.0
CG D:PHE322 4.3 12.7 1.0
NH1 D:ARG26 4.3 9.0 1.0
CE1 D:PHE322 4.3 9.8 1.0
CB D:GLU323 4.4 13.8 1.0
CZ2 D:TRP117 4.4 10.9 1.0
CD D:ARG26 4.5 11.7 1.0
CA D:GLU324 4.6 14.1 1.0
CD2 D:PHE322 4.6 11.1 1.0
CZ D:PHE322 4.7 8.9 1.0
CB D:GLU324 4.7 14.2 1.0
CD D:GLU324 4.8 15.1 1.0
O D:HOH2011 4.8 14.3 1.0
OE2 D:GLU324 4.8 16.6 1.0
CE2 D:PHE322 4.8 10.9 1.0
CB D:PHE322 4.8 13.5 1.0
CG D:LEU29 4.9 12.1 1.0

Calcium binding site 4 out of 7 in 2bs9

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Calcium binding site 4 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 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 Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1503

b:24.7
occ:1.00
 O E:HOH2114 3.1 12.7 1.0
N E:GLU323 3.3 11.2 1.0
NE1 E:TRP117 3.4 11.4 1.0
N E:ARG26 3.4 10.9 1.0
N E:GLU324 3.6 12.4 1.0
CD1 E:LEU29 3.7 10.4 1.0
CA E:GLY25 3.9 10.9 1.0
CG E:GLU324 4.0 13.4 1.0
CA E:GLU323 4.0 11.5 1.0
CG E:ARG26 4.1 11.3 1.0
CD1 E:PHE322 4.1 10.6 1.0
C E:GLU323 4.1 11.7 1.0
CG E:PHE322 4.1 11.5 1.0
C E:GLY25 4.1 10.8 1.0
CD1 E:TRP117 4.1 11.6 1.0
CA E:PHE322 4.1 11.7 1.0
CB E:ARG26 4.2 11.2 1.0
C E:PHE322 4.2 11.5 1.0
CE2 E:TRP117 4.2 11.5 1.0
CE1 E:PHE322 4.2 10.1 1.0
CD2 E:PHE322 4.3 10.9 1.0
CB E:GLU323 4.4 11.4 1.0
CZ E:PHE322 4.4 10.8 1.0
CA E:ARG26 4.4 11.2 1.0
NH1 E:ARG26 4.4 11.9 1.0
CE2 E:PHE322 4.5 11.4 1.0
CA E:GLU324 4.5 12.8 1.0
CZ2 E:TRP117 4.5 12.2 1.0
CD E:ARG26 4.6 10.9 1.0
CB E:GLU324 4.6 13.0 1.0
CB E:PHE322 4.8 11.4 1.0
OE2 E:GLU324 4.9 13.5 1.0
CD E:GLU324 4.9 14.3 1.0
O E:HOH2025 4.9 17.0 1.0
CG E:LEU29 5.0 11.4 1.0

Calcium binding site 5 out of 7 in 2bs9

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Calcium binding site 5 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1503

b:29.0
occ:1.00
 N F:GLU323 3.2 12.4 1.0
O F:HOH2089 3.3 30.2 1.0
NE1 F:TRP117 3.4 15.2 1.0
N F:ARG26 3.4 12.2 1.0
N F:GLU324 3.6 13.6 1.0
CD1 F:LEU29 3.7 10.3 1.0
CG F:GLU324 3.9 13.8 1.0
CA F:GLU323 4.0 12.8 1.0
CG F:ARG26 4.0 12.7 1.0
CB F:ARG26 4.0 12.1 1.0
CG F:PHE322 4.0 13.3 1.0
CA F:GLY25 4.0 12.0 1.0
CE2 F:TRP117 4.1 14.4 1.0
C F:PHE322 4.1 12.4 1.0
CA F:PHE322 4.1 12.5 1.0
CD1 F:PHE322 4.1 13.8 1.0
CD2 F:PHE322 4.1 13.1 1.0
C F:GLU323 4.1 13.4 1.0
CB F:GLU323 4.2 12.9 1.0
CE1 F:PHE322 4.2 12.5 1.0
CE2 F:PHE322 4.2 11.6 1.0
C F:GLY25 4.2 12.1 1.0
CD1 F:TRP117 4.3 15.3 1.0
CZ2 F:TRP117 4.3 14.9 1.0
CZ F:PHE322 4.3 12.5 1.0
CA F:ARG26 4.3 12.3 1.0
CA F:GLU324 4.4 13.9 1.0
NH1 F:ARG26 4.4 12.0 1.0
CB F:PHE322 4.6 12.8 1.0
CB F:GLU324 4.6 13.8 1.0
CG F:LEU29 4.8 11.0 1.0
O F:HOH2006 4.8 23.2 1.0
CD F:ARG26 4.8 13.5 1.0
OE2 F:GLU324 4.9 14.2 1.0
CD F:GLU324 4.9 12.9 1.0

Calcium binding site 6 out of 7 in 2bs9

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Calcium binding site 6 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1503

b:22.2
occ:1.00
 O G:HOH2111 3.2 17.4 1.0
N G:GLU323 3.2 12.2 1.0
NE1 G:TRP117 3.4 11.9 1.0
N G:ARG26 3.4 11.3 1.0
N G:GLU324 3.6 13.3 1.0
CD1 G:LEU29 3.8 8.6 1.0
CA G:GLY25 3.9 11.2 1.0
CA G:GLU323 3.9 12.8 1.0
CG G:ARG26 4.0 10.1 1.0
CG G:GLU324 4.0 14.8 1.0
C G:GLU323 4.0 13.4 1.0
CD1 G:PHE322 4.1 13.2 1.0
CA G:PHE322 4.1 12.5 1.0
CD1 G:TRP117 4.1 12.8 1.0
CG G:PHE322 4.1 13.7 1.0
CB G:ARG26 4.1 10.6 1.0
C G:PHE322 4.2 12.3 1.0
C G:GLY25 4.2 11.6 1.0
CB G:GLU323 4.2 12.9 1.0
CE2 G:TRP117 4.2 11.1 1.0
CE1 G:PHE322 4.2 15.4 1.0
CD2 G:PHE322 4.3 14.2 1.0
NH1 G:ARG26 4.3 9.0 1.0
CZ G:PHE322 4.4 14.3 1.0
CA G:ARG26 4.4 11.3 1.0
CE2 G:PHE322 4.4 15.1 1.0
CA G:GLU324 4.5 13.8 1.0
CZ2 G:TRP117 4.5 10.0 1.0
CD G:ARG26 4.7 8.9 1.0
CB G:GLU324 4.7 13.7 1.0
CB G:PHE322 4.7 12.5 1.0
O G:HOH2013 4.8 12.1 1.0
CD G:GLU324 4.9 17.3 1.0
CG G:LEU29 4.9 9.9 1.0
OE2 G:GLU324 4.9 18.2 1.0

Calcium binding site 7 out of 7 in 2bs9

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Calcium binding site 7 out of 7 in the Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Native Crystal Structure of A GH39 Beta-Xylosidase XYNB1 From Geobacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1503

b:23.0
occ:1.00
 O H:HOH2122 3.2 9.1 1.0
NE1 H:TRP117 3.3 10.8 1.0
N H:GLU323 3.3 12.2 1.0
N H:ARG26 3.4 11.4 1.0
CD1 H:LEU29 3.7 11.4 1.0
N H:GLU324 3.8 11.9 1.0
CB H:ARG26 3.8 11.3 1.0
CE2 H:TRP117 4.0 8.9 1.0
CG H:GLU324 4.0 12.7 1.0
CG H:ARG26 4.0 10.8 1.0
CA H:GLY25 4.0 11.3 1.0
CA H:GLU323 4.1 11.8 1.0
CD1 H:TRP117 4.1 11.2 1.0
C H:GLU323 4.1 11.9 1.0
CA H:PHE322 4.2 12.1 1.0
CA H:ARG26 4.2 11.6 1.0
C H:PHE322 4.2 12.4 1.0
C H:GLY25 4.2 11.3 1.0
CG H:PHE322 4.3 10.9 1.0
CD1 H:PHE322 4.3 10.2 1.0
CZ2 H:TRP117 4.3 9.7 1.0
CB H:GLU323 4.3 11.7 1.0
NH1 H:ARG26 4.4 12.3 1.0
CD2 H:PHE322 4.4 10.1 1.0
CE1 H:PHE322 4.4 9.2 1.0
CD H:ARG26 4.5 9.5 1.0
CZ H:PHE322 4.6 9.1 1.0
CE2 H:PHE322 4.6 9.8 1.0
CA H:GLU324 4.6 12.5 1.0
CB H:GLU324 4.8 11.9 1.0
O H:HOH2010 4.8 15.0 1.0
CB H:PHE322 4.8 12.4 1.0
CG H:LEU29 4.9 11.1 1.0
CD H:GLU324 5.0 12.2 1.0
OE2 H:GLU324 5.0 14.4 1.0
O H:GLU323 5.0 11.2 1.0

Reference:

M.Czjzek, A.B.David, T.Bravman, G.Shoham, B.Henrissat, Y.Shoham. Enzyme-Substrate Complex Structures of A GH39 Beta- Xylosidase From Geobacillus Stearothermophilus. J.Mol.Biol. V. 353 838 2005.
ISSN: ISSN 0022-2836
PubMed: 16212978
DOI: 10.1016/J.JMB.2005.09.003
Page generated: Tue Jul 8 04:37:06 2025

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