Sodium in PDB 5glq: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free 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-Free Form, PDB code: 5glq 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)	78.65 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.801, 61.489, 79.047, 90.00, 95.72, 90.00
R / Rfree (%)	14.9 / 17.5

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-Free Form (pdb code 5glq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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-Free Form, PDB code: 5glq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free 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-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.4 occ:1.00 O A:HOH775 2.2 13.8 1.0 O A:HOH615 2.3 10.6 1.0 O A:HOH705 2.3 10.2 1.0 O A:HOH564 2.4 12.7 1.0 O A:ALA270 2.7 9.3 1.0 NE2 A:HIS319 3.5 11.3 1.0 CE3 A:TRP271 3.7 9.2 1.0 C A:ALA270 3.8 9.3 1.0 OG A:SER59 4.0 9.9 1.0 O A:HIS320 4.1 8.8 1.0 O A:HOH612 4.1 10.7 1.0 C A:ALA269 4.2 9.0 1.0 O A:ALA269 4.2 8.9 1.0 CE1 A:HIS319 4.2 10.9 1.0 CB A:ALA179 4.2 9.9 1.0 CB A:TRP271 4.3 9.1 1.0 CD2 A:HIS319 4.4 10.9 1.0 O A:PRO178 4.4 10.2 1.0 CZ3 A:TRP271 4.4 9.4 1.0 CA A:ALA269 4.5 9.2 1.0 N A:ALA270 4.5 8.9 1.0 N A:TRP271 4.5 9.1 1.0 CA A:TRP271 4.5 9.2 1.0 CD2 A:TRP271 4.6 9.1 1.0 O A:HOH524 4.6 13.4 1.0 CA A:ALA270 4.8 9.1 1.0 CG A:TRP271 4.9 8.9 1.0 CB A:ALA269 4.9 8.9 1.0 CA A:ALA179 4.9 9.7 1.0 O A:ASP177 5.0 9.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free 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-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.3 occ:1.00 O B:HOH538 2.3 31.4 1.0 OG1 A:THR363 2.4 11.9 1.0 O B:HOH746 2.4 38.0 1.0 O B:HOH622 2.4 15.8 1.0 O A:HOH602 2.5 16.3 1.0 O A:HOH771 2.5 28.6 1.0 CB A:THR363 3.7 11.9 1.0 O A:HOH770 3.8 40.3 1.0 O A:HOH816 3.9 28.8 1.0 O A:HOH541 4.0 22.4 1.0 O B:HOH582 4.0 21.6 1.0 O A:VAL308 4.1 10.8 1.0 N A:THR363 4.1 12.5 1.0 O A:ILE361 4.2 13.3 1.0 OD1 B:ASP263 4.4 21.1 1.0 OD2 B:ASP263 4.4 23.3 1.0 CA A:THR363 4.4 12.1 1.0 N A:VAL308 4.5 10.2 1.0 CG2 A:THR363 4.7 11.9 1.0 CG B:ASP263 4.8 20.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free Form


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 COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:21.3 occ:1.00 O B:HOH697 2.2 16.1 1.0 O B:HOH616 2.3 13.4 1.0 O B:HOH675 2.4 12.5 1.0 O B:HOH514 2.4 15.5 1.0 O B:ALA270 2.8 12.5 1.0 NE2 B:HIS319 3.5 13.0 1.0 CE3 B:TRP271 3.7 11.6 1.0 C B:ALA270 3.9 11.8 1.0 OG B:SER59 4.0 12.2 1.0 O B:HOH565 4.1 14.1 1.0 O B:HIS320 4.1 11.7 1.0 CE1 B:HIS319 4.1 12.9 1.0 C B:ALA269 4.2 10.8 1.0 CB B:ALA179 4.2 13.0 1.0 O B:ALA269 4.3 11.1 1.0 CB B:TRP271 4.4 11.6 1.0 O B:PRO178 4.4 13.1 1.0 CD2 B:HIS319 4.4 12.7 1.0 CZ3 B:TRP271 4.4 11.3 1.0 CA B:ALA269 4.5 11.1 1.0 N B:ALA270 4.5 11.0 1.0 CD2 B:TRP271 4.6 11.3 1.0 CA B:TRP271 4.6 11.9 1.0 N B:TRP271 4.6 11.6 1.0 O B:HOH512 4.7 16.4 1.0 CA B:ALA270 4.8 11.4 1.0 CA B:ALA179 4.9 13.0 1.0 CG B:TRP271 4.9 11.2 1.0 CB B:ALA269 4.9 11.6 1.0 O B:ASP177 5.0 12.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free Form


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 COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:25.2 occ:1.00 O A:HOH575 2.4 31.7 1.0 O B:HOH595 2.4 22.1 1.0 O B:HOH693 2.5 25.9 1.0 OG1 B:THR363 2.5 17.4 1.0 O A:HOH668 2.6 20.7 1.0 CB B:THR363 3.8 17.3 1.0 O B:HOH739 3.9 31.4 1.0 N B:THR363 4.1 17.6 1.0 O B:VAL308 4.1 15.1 1.0 O B:ILE361 4.1 19.7 1.0 O B:HOH503 4.2 26.4 1.0 O A:HOH686 4.3 19.8 1.0 OD1 A:ASP263 4.4 17.4 1.0 CA B:THR363 4.5 17.2 1.0 OD2 A:ASP263 4.5 18.9 1.0 O A:HOH800 4.6 33.5 1.0 N B:VAL308 4.7 14.7 1.0 CG2 B:THR363 4.9 17.1 1.0 CG A:ASP263 4.9 16.0 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