Atomistry » Calcium » PDB 2bir-2bw1 » 2bs9
Atomistry »
  Calcium »
    PDB 2bir-2bw1 »
      2bs9 »

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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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

Go back to Calcium Binding Sites List in 2bs9
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: Fri Jul 12 09:10:59 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