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Sodium in PDB 2bfg: Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside

Enzymatic activity of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside

All present enzymatic activity of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside:
3.2.1.37;

Protein crystallography data

The structure of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside, PDB code: 2bfg 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) 40.11 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.950, 162.160, 308.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 27

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside (pdb code 2bfg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside, PDB code: 2bfg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2bfg

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Sodium binding site 1 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1503

b:19.2
occ:1.00
 N D:GLU323 3.2 18.8 1.0
NE1 D:TRP117 3.3 18.8 1.0
O D:HOH2106 3.3 13.2 1.0
N D:ARG26 3.4 18.8 1.0
N D:GLU324 3.6 19.5 1.0
CG D:GLU324 3.9 17.9 1.0
CG D:ARG26 3.9 18.8 1.0
CD1 D:LEU29 3.9 21.0 1.0
CB D:ARG26 3.9 18.2 1.0
CD1 D:TRP117 4.0 18.1 1.0
CA D:GLY25 4.0 19.3 1.0
CA D:GLU323 4.0 19.0 1.0
CE2 D:TRP117 4.1 17.3 1.0
NH1 D:ARG26 4.1 15.7 1.0
CA D:PHE322 4.1 17.9 1.0
CG D:PHE322 4.1 15.9 1.0
C D:PHE322 4.1 18.0 1.0
CD1 D:PHE322 4.1 11.8 1.0
C D:GLU323 4.2 19.5 1.0
C D:GLY25 4.2 18.8 1.0
CB D:GLU323 4.2 18.9 1.0
CA D:ARG26 4.3 18.5 1.0
CD2 D:PHE322 4.3 14.7 1.0
CE1 D:PHE322 4.3 12.7 1.0
CZ2 D:TRP117 4.4 18.1 1.0
CE2 D:PHE322 4.5 14.7 1.0
CZ D:PHE322 4.5 12.1 1.0
CA D:GLU324 4.5 19.7 1.0
CD D:ARG26 4.7 19.3 1.0
CB D:GLU324 4.7 19.6 1.0
CB D:PHE322 4.7 17.7 1.0
OE2 D:GLU324 4.8 16.2 1.0
CG D:LEU29 4.8 18.5 1.0
CD D:GLU324 4.8 17.2 1.0
O D:HOH2013 4.9 35.5 1.0
CG D:TRP117 5.0 20.1 1.0

Sodium binding site 2 out of 8 in 2bfg

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Sodium binding site 2 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1503

b:5.2
occ:1.00
 O E:HOH2124 3.1 26.8 1.0
N E:GLU323 3.2 18.4 1.0
NE1 E:TRP117 3.3 22.5 1.0
N E:ARG26 3.5 18.7 1.0
N E:GLU324 3.6 19.4 1.0
CD1 E:LEU29 3.9 17.9 1.0
CG E:GLU324 3.9 19.9 1.0
CA E:GLY25 3.9 18.7 1.0
CD1 E:TRP117 4.0 23.2 1.0
CA E:PHE322 4.0 17.7 1.0
CG E:PHE322 4.0 16.1 1.0
CA E:GLU323 4.0 18.5 1.0
C E:GLU323 4.1 19.0 1.0
CG E:ARG26 4.1 20.8 1.0
C E:PHE322 4.1 17.9 1.0
CB E:ARG26 4.1 18.6 1.0
CD2 E:PHE322 4.1 19.8 1.0
CE2 E:TRP117 4.1 24.5 1.0
CD1 E:PHE322 4.2 17.4 1.0
C E:GLY25 4.2 18.6 1.0
CE2 E:PHE322 4.3 21.1 1.0
CB E:GLU323 4.3 18.5 1.0
CE1 E:PHE322 4.3 18.7 1.0
NH1 E:ARG26 4.4 23.6 1.0
CA E:ARG26 4.4 18.3 1.0
CZ E:PHE322 4.4 19.6 1.0
CD E:ARG26 4.4 22.3 1.0
CA E:GLU324 4.4 19.2 1.0
CZ2 E:TRP117 4.6 23.9 1.0
CB E:GLU324 4.6 19.0 1.0
CB E:PHE322 4.6 18.5 1.0
O E:HOH2010 4.7 24.0 1.0
CG E:LEU29 4.9 16.6 1.0
OE2 E:GLU324 4.9 18.7 1.0
CD E:GLU324 4.9 21.3 1.0
O E:GLU323 5.0 19.5 1.0

Sodium binding site 3 out of 8 in 2bfg

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Sodium binding site 3 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1503

b:7.3
occ:1.00
 O G:HOH2110 3.1 26.3 1.0
N G:GLU323 3.2 18.5 1.0
N G:ARG26 3.4 18.7 1.0
NE1 G:TRP117 3.4 16.7 1.0
N G:GLU324 3.6 18.8 1.0
CD1 G:LEU29 3.7 18.1 1.0
CA G:GLY25 3.8 18.7 1.0
CG G:GLU324 4.0 17.2 1.0
CA G:PHE322 4.0 17.8 1.0
CG G:ARG26 4.0 17.9 1.0
CA G:GLU323 4.0 18.9 1.0
NH1 G:ARG26 4.0 17.5 1.0
CG G:PHE322 4.0 15.7 1.0
C G:GLU323 4.0 19.0 1.0
CD1 G:TRP117 4.1 17.8 1.0
C G:PHE322 4.1 18.1 1.0
C G:GLY25 4.1 18.7 1.0
CD1 G:PHE322 4.1 13.4 1.0
CD2 G:PHE322 4.1 15.0 1.0
CB G:GLU323 4.1 19.0 1.0
CB G:ARG26 4.2 18.1 1.0
CE2 G:TRP117 4.2 16.8 1.0
CE1 G:PHE322 4.3 15.3 1.0
CE2 G:PHE322 4.3 15.6 1.0
CA G:ARG26 4.4 18.5 1.0
CZ G:PHE322 4.4 15.0 1.0
CA G:GLU324 4.4 19.3 1.0
CB G:PHE322 4.6 18.3 1.0
CD G:ARG26 4.6 17.8 1.0
CB G:GLU324 4.6 19.2 1.0
CZ2 G:TRP117 4.6 18.4 1.0
CD G:GLU324 4.8 17.8 1.0
CG G:LEU29 4.9 17.2 1.0
O G:GLU323 4.9 20.5 1.0
O G:HOH2024 5.0 20.2 1.0

Sodium binding site 4 out of 8 in 2bfg

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Sodium binding site 4 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1503

b:10.2
occ:1.00
 O C:HOH2121 3.2 21.0 1.0
NE1 C:TRP117 3.2 21.1 1.0
N C:GLU323 3.3 18.2 1.0
N C:ARG26 3.3 19.3 1.0
N C:GLU324 3.7 18.7 1.0
CD1 C:LEU29 3.8 18.9 1.0
CG C:ARG26 3.9 17.9 1.0
CD1 C:TRP117 3.9 20.0 1.0
CA C:GLY25 3.9 19.3 1.0
NH1 C:ARG26 3.9 24.6 1.0
CB C:ARG26 4.0 18.1 1.0
CA C:GLU323 4.0 18.7 1.0
CG C:GLU324 4.0 18.6 1.0
CA C:PHE322 4.0 17.9 1.0
CE2 C:TRP117 4.0 19.5 1.0
C C:PHE322 4.1 18.0 1.0
C C:GLY25 4.1 19.8 1.0
CD1 C:PHE322 4.1 12.6 1.0
C C:GLU323 4.1 18.6 1.0
CG C:PHE322 4.1 15.8 1.0
CB C:GLU323 4.1 19.1 1.0
CA C:ARG26 4.3 18.6 1.0
CE1 C:PHE322 4.3 16.1 1.0
CD2 C:PHE322 4.3 16.5 1.0
CD C:ARG26 4.3 18.8 1.0
CA C:GLU324 4.5 18.9 1.0
CZ C:PHE322 4.5 16.8 1.0
CZ2 C:TRP117 4.5 20.3 1.0
CE2 C:PHE322 4.5 16.7 1.0
CB C:PHE322 4.7 18.3 1.0
CB C:GLU324 4.7 18.6 1.0
CG C:LEU29 4.7 17.4 1.0
O C:HOH2012 4.8 19.4 1.0
CG C:TRP117 4.9 20.8 1.0
CD C:GLU324 4.9 17.2 1.0
CZ C:ARG26 5.0 22.7 1.0
CD2 C:TRP117 5.0 19.6 1.0

Sodium binding site 5 out of 8 in 2bfg

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Sodium binding site 5 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1503

b:6.2
occ:1.00
 O B:HOH2104 3.0 17.5 1.0
NE1 B:TRP117 3.2 24.1 1.0
N B:ARG26 3.3 18.6 1.0
N B:GLU323 3.4 18.0 1.0
N B:GLU324 3.6 19.4 1.0
CG B:ARG26 3.8 17.9 1.0
CA B:GLY25 3.8 19.0 1.0
CG B:GLU324 3.9 19.4 1.0
CD1 B:TRP117 3.9 25.5 1.0
CD1 B:LEU29 3.9 15.4 1.0
CA B:PHE322 4.0 18.1 1.0
CB B:ARG26 4.0 18.0 1.0
C B:GLY25 4.1 18.0 1.0
CG B:PHE322 4.1 16.3 1.0
CD1 B:PHE322 4.1 16.4 1.0
CE2 B:TRP117 4.1 23.8 1.0
C B:GLU323 4.2 19.1 1.0
C B:PHE322 4.2 18.0 1.0
NH1 B:ARG26 4.2 21.8 1.0
CA B:GLU323 4.2 18.2 1.0
CD2 B:PHE322 4.2 17.6 1.0
CE1 B:PHE322 4.3 17.3 1.0
CA B:ARG26 4.3 18.1 1.0
CE2 B:PHE322 4.3 18.5 1.0
CA B:GLU324 4.4 19.6 1.0
CZ B:PHE322 4.4 16.1 1.0
CB B:GLU323 4.4 18.2 1.0
CB B:GLU324 4.5 19.4 1.0
CZ2 B:TRP117 4.6 25.5 1.0
CD B:ARG26 4.6 18.9 1.0
CB B:PHE322 4.6 18.3 1.0
CG B:LEU29 4.7 15.3 1.0
CD B:GLU324 4.8 20.3 1.0
O B:HOH2010 4.8 20.6 1.0
OE2 B:GLU324 4.8 16.1 1.0
CG B:TRP117 4.9 25.7 1.0

Sodium binding site 6 out of 8 in 2bfg

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Sodium binding site 6 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1503

b:9.8
occ:1.00
 NE1 H:TRP117 3.0 17.0 1.0
O H:HOH2122 3.1 15.0 1.0
N H:ARG26 3.2 18.1 1.0
N H:GLU323 3.3 19.0 1.0
N H:GLU324 3.7 19.2 1.0
CG H:ARG26 3.8 18.8 1.0
CD1 H:TRP117 3.8 17.7 1.0
CB H:ARG26 3.8 18.2 1.0
CE2 H:TRP117 3.8 16.9 1.0
CD1 H:LEU29 3.8 18.0 1.0
CA H:GLY25 3.9 19.4 1.0
CG H:GLU324 4.0 18.7 1.0
C H:GLY25 4.0 19.0 1.0
CA H:GLU323 4.1 19.1 1.0
CA H:ARG26 4.1 18.4 1.0
C H:GLU323 4.1 19.0 1.0
CA H:PHE322 4.2 18.1 1.0
C H:PHE322 4.2 18.4 1.0
CZ2 H:TRP117 4.2 14.9 1.0
CD H:ARG26 4.2 19.4 1.0
CG H:PHE322 4.3 16.0 1.0
CB H:GLU323 4.3 19.4 1.0
NH1 H:ARG26 4.3 22.6 1.0
CD2 H:PHE322 4.4 14.3 1.0
CD1 H:PHE322 4.4 16.2 1.0
CA H:GLU324 4.5 19.5 1.0
CE2 H:PHE322 4.6 14.5 1.0
CE1 H:PHE322 4.6 14.8 1.0
CZ H:PHE322 4.6 15.0 1.0
O H:HOH2010 4.8 22.8 1.0
CB H:GLU324 4.8 18.9 1.0
CG H:TRP117 4.8 18.4 1.0
CG H:LEU29 4.8 17.7 1.0
CD2 H:TRP117 4.8 17.1 1.0
CB H:PHE322 4.9 18.2 1.0
CD H:GLU324 4.9 17.9 1.0
OE2 H:GLU324 5.0 21.6 1.0

Sodium binding site 7 out of 8 in 2bfg

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Sodium binding site 7 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1503

b:9.1
occ:1.00
 O A:HOH2119 3.1 24.3 1.0
N A:GLU323 3.2 18.2 1.0
NE1 A:TRP117 3.2 20.6 1.0
N A:ARG26 3.4 18.3 1.0
N A:GLU324 3.5 19.2 1.0
CG A:GLU324 3.8 19.6 1.0
CG A:ARG26 3.8 18.2 1.0
CD1 A:TRP117 3.9 20.1 1.0
CA A:GLY25 3.9 19.1 1.0
CD1 A:LEU29 3.9 18.1 1.0
C A:GLU323 4.0 18.8 1.0
CA A:GLU323 4.0 18.3 1.0
CA A:PHE322 4.1 17.6 1.0
CE2 A:TRP117 4.1 20.4 1.0
CG A:PHE322 4.1 15.8 1.0
C A:PHE322 4.1 17.2 1.0
CB A:ARG26 4.2 18.4 1.0
C A:GLY25 4.2 18.3 1.0
CD1 A:PHE322 4.2 14.1 1.0
CD2 A:PHE322 4.2 19.7 1.0
NH1 A:ARG26 4.2 21.9 1.0
CA A:GLU324 4.3 19.7 1.0
CE2 A:PHE322 4.3 20.2 1.0
CE1 A:PHE322 4.3 14.3 1.0
CB A:GLU323 4.4 18.9 1.0
CA A:ARG26 4.4 18.3 1.0
CZ A:PHE322 4.4 17.8 1.0
CB A:GLU324 4.5 20.1 1.0
CZ2 A:TRP117 4.5 20.1 1.0
CB A:PHE322 4.7 18.2 1.0
CD A:ARG26 4.7 18.5 1.0
CD A:GLU324 4.8 20.4 1.0
O A:HOH2008 4.8 19.6 1.0
OE2 A:GLU324 4.8 19.2 1.0
CG A:LEU29 4.9 15.9 1.0
O A:GLU323 4.9 19.0 1.0
CG A:TRP117 4.9 22.1 1.0

Sodium binding site 8 out of 8 in 2bfg

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Sodium binding site 8 out of 8 in the Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Beta-Xylosidase (Fam GH39) in Complex with Dinitrophenyl-Beta-Xyloside and Covalently Bound Xyloside within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1503

b:4.6
occ:1.00
 O F:HOH2094 3.1 21.0 1.0
NE1 F:TRP117 3.2 26.1 1.0
N F:GLU323 3.3 19.3 1.0
N F:ARG26 3.3 18.6 1.0
N F:GLU324 3.7 20.0 1.0
CD1 F:LEU29 3.8 19.1 1.0
CG F:GLU324 3.9 19.2 1.0
CD1 F:TRP117 3.9 25.9 1.0
CG F:ARG26 3.9 20.5 1.0
CB F:ARG26 3.9 19.0 1.0
CA F:GLY25 4.0 19.6 1.0
CE2 F:TRP117 4.0 25.2 1.0
CA F:GLU323 4.1 19.9 1.0
NH1 F:ARG26 4.1 19.8 1.0
C F:GLY25 4.1 19.1 1.0
CA F:PHE322 4.2 18.5 1.0
C F:GLU323 4.2 19.8 1.0
CD1 F:PHE322 4.2 18.3 1.0
CG F:PHE322 4.2 18.3 1.0
C F:PHE322 4.2 18.7 1.0
CA F:ARG26 4.2 18.7 1.0
CB F:GLU323 4.3 20.0 1.0
CE1 F:PHE322 4.3 17.1 1.0
CD2 F:PHE322 4.3 19.2 1.0
CZ2 F:TRP117 4.4 25.8 1.0
CD F:ARG26 4.5 22.7 1.0
CA F:GLU324 4.5 20.1 1.0
CE2 F:PHE322 4.5 18.0 1.0
CZ F:PHE322 4.5 16.0 1.0
CB F:GLU324 4.6 20.1 1.0
CG F:LEU29 4.6 19.8 1.0
CD F:GLU324 4.8 16.8 1.0
CB F:PHE322 4.8 19.1 1.0
OE2 F:GLU324 4.8 15.7 1.0
O F:HOH2006 4.8 22.5 1.0
CG F:TRP117 5.0 24.5 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: Mon Oct 7 01:58:58 2024

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