Calcium in PDB 2x8f: 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;

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

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

Sodium

(Na)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis, PDB code: 2x8f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1472 b:14.1 occ:1.00 O A:HOH2104 2.4 11.7 1.0 O A:HOH2012 2.4 11.4 1.0 O A:HOH2144 2.5 10.9 1.0 NE2 A:HIS318 2.5 10.8 1.0 O A:HOH2194 2.5 12.6 1.0 O A:HOH2105 2.6 11.4 1.0 O A:HOH2009 2.6 17.0 1.0 CD2 A:HIS318 3.3 12.9 1.0 CE1 A:HIS318 3.6 10.5 1.0 O A:PRO172 4.0 13.6 1.0 O A:PRO226 4.5 14.0 1.0 O A:ASN319 4.5 12.9 1.0 O A:ALA102 4.5 14.1 1.0 CG A:HIS318 4.6 13.0 1.0 CB A:ALA101 4.6 10.9 1.0 O A:ASP38 4.6 15.4 1.0 OG A:SER40 4.6 13.0 1.0 ND1 A:HIS318 4.6 12.9 1.0 CB A:SER40 4.7 12.4 1.0 CD1 A:TYR227 4.8 10.8 1.0 O A:ASP171 4.8 13.6 1.0 CA A:GLY225 4.9 10.3 1.0 C A:ASP171 4.9 11.4 1.0 C A:PRO172 4.9 15.7 1.0

Calcium binding site 2 out of 2 in the Native Structure of Endo-1,5-Alpha-L-Arabinanases From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca1473 b:11.8 occ:1.00 O B:HOH2016 2.4 10.0 1.0 O B:HOH2014 2.4 9.4 1.0 O B:HOH2012 2.5 11.2 1.0 O B:HOH2203 2.5 9.6 1.0 O B:HOH2105 2.5 10.7 1.0 O B:HOH2148 2.5 10.6 1.0 NE2 B:HIS318 2.5 9.6 1.0 CD2 B:HIS318 3.3 9.6 1.0 CE1 B:HIS318 3.6 11.0 1.0 O B:PRO172 4.0 12.1 1.0 O B:ALA102 4.5 14.8 1.0 O B:PRO226 4.5 13.7 1.0 O B:ASN319 4.5 12.5 1.0 OG B:SER40 4.6 12.6 1.0 CG B:HIS318 4.6 11.7 1.0 O B:ASP38 4.6 10.5 1.0 CB B:ALA101 4.6 10.3 1.0 CB B:SER40 4.6 13.3 1.0 ND1 B:HIS318 4.7 11.4 1.0 CD1 B:TYR227 4.8 10.9 1.0 O B:ASP171 4.9 11.3 1.0 C B:PRO172 4.9 14.9 1.0 CA B:GLY225 4.9 11.1 1.0 C B:ASP171 4.9 12.1 1.0

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