Atomistry » Sodium » PDB 2aoe-2bhp » 2bfg
Atomistry »
  Sodium »
    PDB 2aoe-2bhp »
      2bfg »

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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Go back to Sodium Binding Sites List in 2bfg
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy