Sodium in PDB 5glr: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form, PDB code: 5glr was solved by T.Matsuzawa, N.Kishine, Z.Fujimoto, K.Yaoi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.60 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.929, 61.343, 79.001, 90.00, 95.79, 90.00
R / Rfree (%)	15.1 / 17.5

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form (pdb code 5glr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form, PDB code: 5glr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form


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 COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:23.2 occ:1.00 O B:HOH557 2.3 28.6 1.0 O B:HOH743 2.4 33.9 1.0 OG1 A:THR363 2.4 13.0 1.0 O B:HOH653 2.4 15.8 1.0 O A:HOH605 2.5 18.0 1.0 O A:HOH769 2.6 28.9 1.0 CB A:THR363 3.7 12.4 1.0 O A:HOH779 3.8 31.4 1.0 O A:HOH546 4.0 23.7 1.0 O A:HOH824 4.0 28.2 1.0 O B:HOH596 4.1 21.1 1.0 O A:VAL308 4.1 11.1 1.0 N A:THR363 4.2 12.6 1.0 O A:ILE361 4.3 13.4 1.0 OD1 B:ASP263 4.4 21.5 1.0 OD2 B:ASP263 4.4 25.6 1.0 CA A:THR363 4.5 12.5 1.0 N A:VAL308 4.5 10.2 1.0 CG2 A:THR363 4.7 12.6 1.0 CG B:ASP263 4.8 22.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form


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 COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:24.2 occ:1.00 O A:HOH594 2.3 32.4 1.0 O B:HOH563 2.4 21.1 1.0 O B:HOH700 2.5 28.8 1.0 OG1 B:THR363 2.5 17.9 1.0 O B:HOH655 2.6 21.0 1.0 CB B:THR363 3.7 17.9 1.0 O B:HOH736 3.9 29.5 1.0 O B:ILE361 4.1 18.6 1.0 N B:THR363 4.1 17.7 1.0 O B:VAL308 4.1 15.1 1.0 O B:HOH502 4.1 24.9 1.0 O A:HOH674 4.3 19.3 1.0 O A:HOH806 4.4 34.8 1.0 OD1 A:ASP263 4.4 17.6 1.0 CA B:THR363 4.5 17.8 1.0 OD2 A:ASP263 4.6 20.7 1.0 N B:VAL308 4.6 14.9 1.0 CG2 B:THR363 4.8 17.8 1.0 CG A:ASP263 4.9 17.1 1.0

T.Matsuzawa, S.Kaneko, N.Kishine, Z.Fujimoto, K.Yaoi. Crystal Structure of Metagenomic Beta-Xylosidase/ Alpha-L-Arabinofuranosidase Activated By Calcium. J. Biochem. V. 162 173 2017.
ISSN: ISSN 1756-2651
PubMed: 28204531
DOI: 10.1093/JB/MVX012