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Sodium in PDB 2x8f: Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis

Enzymatic activity of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis

All present enzymatic activity of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis:
3.2.1.99;

Protein crystallography data

The structure of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis, PDB code: 2x8f was solved by D.De Sanctis, J.M.Inacio, P.F.Lindley, I.De Sa-Nogueira, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.62 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.975, 57.645, 86.272, 82.31, 87.97, 63.66
R / Rfree (%) 14.1 / 18

Other elements in 2x8f:

The structure of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis (pdb code 2x8f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis, PDB code: 2x8f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2x8f

Go back to Sodium Binding Sites List in 2x8f
Sodium binding site 1 out of 4 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1474

b:21.7
occ:1.00
 O A:HOH2015 2.5 13.8 1.0
O A:HOH2016 2.5 16.6 1.0
O A:VAL104 2.5 15.0 1.0
OD1 A:ASP103 2.6 14.9 1.0
OG1 A:THR105 2.6 15.1 1.0
OD2 A:ASP103 3.0 15.3 1.0
CG A:ASP103 3.1 14.3 1.0
O A:HOH2107 3.2 19.9 1.0
C A:VAL104 3.4 15.7 1.0
CB A:THR105 3.7 18.3 1.0
CA A:THR105 3.8 15.1 1.0
O A:HOH2013 3.9 18.2 1.0
N A:THR105 3.9 12.8 1.0
N A:VAL104 4.0 12.0 1.0
O A:THR174 4.1 16.1 1.0
OG A:SER40 4.2 13.0 1.0
O A:ILE41 4.3 16.1 1.0
CD2 A:HIS173 4.3 11.9 1.0
O A:HOH2014 4.3 17.7 1.0
CA A:VAL104 4.4 12.4 1.0
CG2 A:THR105 4.4 13.3 1.0
NE2 A:HIS173 4.5 13.5 1.0
CB A:ASP103 4.6 15.3 1.0
OH A:TYR227 4.7 13.1 1.0
C A:ASP103 4.8 17.3 1.0
CB A:ILE42 4.8 15.4 1.0
O A:HOH2065 5.0 30.0 1.0

Sodium binding site 2 out of 4 in 2x8f

Go back to Sodium Binding Sites List in 2x8f
Sodium binding site 2 out of 4 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1475

b:21.7
occ:1.00
 O A:VAL73 2.4 15.8 1.0
OH A:TYR84 2.5 16.1 1.0
O A:HOH2058 2.5 20.3 1.0
O A:HOH2059 2.7 21.3 1.0
C A:VAL73 3.6 17.6 1.0
CZ A:TYR84 3.6 18.4 1.0
CE2 A:TYR84 4.0 16.8 1.0
O A:ASP97 4.0 19.7 1.0
O A:HOH2042 4.3 29.6 1.0
CB A:VAL73 4.4 16.3 1.0
CA A:SER74 4.5 24.8 1.0
CA A:VAL73 4.5 16.7 1.0
N A:SER74 4.5 18.2 1.0
CG1 A:VAL73 4.7 14.9 1.0
CB A:SER74 4.7 32.1 1.0
O A:HOH2043 4.7 16.0 1.0
N A:VAL73 4.7 17.5 1.0
OD2 A:ASP97 4.8 24.0 1.0
CE1 A:TYR84 4.8 16.7 1.0
CB A:ASP97 5.0 15.9 1.0

Sodium binding site 3 out of 4 in 2x8f

Go back to Sodium Binding Sites List in 2x8f
Sodium binding site 3 out of 4 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1474

b:17.1
occ:1.00
 O B:VAL104 2.5 14.1 1.0
OD1 B:ASP103 2.5 14.3 1.0
OG1 B:THR105 2.5 14.2 1.0
O B:HOH2036 2.5 15.7 1.0
O B:HOH2018 2.6 12.9 1.0
CG B:ASP103 3.2 17.6 1.0
OD2 B:ASP103 3.2 19.1 1.0
O B:HOH2106 3.2 17.9 1.0
C B:VAL104 3.3 10.9 1.0
CB B:THR105 3.7 14.8 1.0
O B:HOH2015 3.7 14.8 1.0
CA B:THR105 3.7 11.1 1.0
N B:THR105 3.8 11.0 1.0
N B:VAL104 4.0 10.4 1.0
O B:THR174 4.2 13.3 1.0
O B:ILE41 4.2 14.6 1.0
OG B:SER40 4.3 12.6 1.0
CD2 B:HIS173 4.3 12.3 1.0
CA B:VAL104 4.3 11.9 1.0
O B:HOH2017 4.3 16.4 1.0
CG2 B:THR105 4.4 13.0 1.0
NE2 B:HIS173 4.5 12.2 1.0
CB B:ASP103 4.6 11.7 1.0
C B:ASP103 4.7 13.3 1.0
OH B:TYR227 4.7 13.4 1.0
O B:HOH2069 4.8 17.1 1.0
CB B:ILE42 4.8 14.5 1.0
CA B:ASP103 4.9 12.3 1.0

Sodium binding site 4 out of 4 in 2x8f

Go back to Sodium Binding Sites List in 2x8f
Sodium binding site 4 out of 4 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1475

b:19.4
occ:1.00
 O B:VAL73 2.4 17.2 1.0
OH B:TYR84 2.5 15.8 1.0
O B:HOH2060 2.5 12.7 1.0
O B:HOH2061 2.6 16.2 1.0
CZ B:TYR84 3.6 17.7 1.0
C B:VAL73 3.6 18.1 1.0
CE2 B:TYR84 4.0 16.9 1.0
O B:ASP97 4.0 15.8 1.0
CB B:VAL73 4.4 15.0 1.0
CA B:SER74 4.5 19.2 1.0
CA B:VAL73 4.5 12.8 1.0
N B:SER74 4.5 14.8 1.0
O B:HOH2041 4.5 25.1 1.0
CG1 B:VAL73 4.6 12.9 1.0
O B:HOH2064 4.7 14.8 1.0
CB B:SER74 4.7 26.7 1.0
N B:VAL73 4.8 12.7 1.0
OD1 B:ASP97 4.8 19.8 1.0
CE1 B:TYR84 4.8 17.0 1.0
CB B:ASP97 5.0 16.0 1.0

Reference:

D.De Sanctis, J.M.Inacio, P.F.Lindley, I.De Sa-Nogueira, I.Bento. New Evidence For the Role of Calcium in the Glycosidase Reaction of GH43 Arabinanases. Febs J. V. 277 4562 2010.
ISSN: ISSN 1742-464X
PubMed: 20883454
DOI: 10.1111/J.1742-4658.2010.07870.X
Page generated: Mon Oct 7 05:06:05 2024

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