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

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free Form, PDB code: 5glo 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)	78.89 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.764, 61.385, 79.239, 90.00, 95.41, 90.00
R / Rfree (%)	15.5 / 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, Calcium-Free Form (pdb code 5glo). 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, Calcium-Free Form, PDB code: 5glo:
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, 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, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:18.8 occ:1.00 O A:HOH682 2.3 16.6 1.0 O A:HOH734 2.3 14.1 1.0 O A:HOH615 2.4 13.6 1.0 O A:HOH533 2.4 15.1 1.0 O A:HOH501 2.4 21.3 1.0 O A:ALA270 3.2 11.9 1.0 NE2 A:HIS319 3.5 14.5 1.0 OG A:SER59 3.8 13.0 1.0 CE3 A:TRP271 3.8 11.6 1.0 O A:HOH534 4.0 14.2 1.0 O A:HIS320 4.2 13.7 1.0 C A:ALA270 4.2 12.1 1.0 CE1 A:HIS319 4.3 14.5 1.0 CD2 A:HIS319 4.3 14.6 1.0 O A:PRO178 4.3 12.3 1.0 C A:ALA269 4.4 12.4 1.0 CB A:ALA179 4.4 12.8 1.0 CZ3 A:TRP271 4.4 11.5 1.0 O A:ALA269 4.5 12.5 1.0 CA A:ALA269 4.5 12.7 1.0 O A:HOH504 4.5 15.1 1.0 CB A:TRP271 4.7 11.6 1.0 N A:ALA270 4.8 12.1 1.0 CD2 A:TRP271 4.8 11.4 1.0 CB A:ALA269 4.9 12.6 1.0 CA A:TRP271 4.9 11.6 1.0 N A:TRP271 5.0 11.8 1.0 O A:ASP177 5.0 13.4 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, 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, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:32.0 occ:1.00 O B:HOH544 2.3 32.9 1.0 O B:HOH801 2.4 46.2 1.0 OG1 A:THR363 2.4 14.7 1.0 O B:HOH546 2.4 18.6 1.0 O A:HOH594 2.5 19.4 1.0 O A:HOH775 2.5 30.4 1.0 CB A:THR363 3.7 14.9 1.0 O A:HOH747 3.7 43.3 1.0 O A:HOH824 3.9 44.8 1.0 O A:HOH507 4.1 28.6 1.0 O A:VAL308 4.1 14.1 1.0 O B:HOH610 4.1 25.0 1.0 N A:THR363 4.1 14.9 1.0 O A:ILE361 4.2 15.7 1.0 OD1 B:ASP263 4.3 26.0 1.0 OD2 B:ASP263 4.3 26.3 1.0 N A:VAL308 4.4 13.6 1.0 CA A:THR363 4.4 14.7 1.0 CG2 A:THR363 4.7 14.9 1.0 CG B:ASP263 4.7 25.4 1.0 C A:VAL308 5.0 14.0 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, 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, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:21.5 occ:1.00 O B:HOH612 2.2 17.9 1.0 O B:HOH669 2.3 14.7 1.0 O B:HOH579 2.4 18.0 1.0 O B:HOH613 2.4 14.4 1.0 O B:HOH510 2.4 21.3 1.0 O B:ALA270 3.2 15.7 1.0 NE2 B:HIS319 3.4 15.7 1.0 OG B:SER59 3.7 15.6 1.0 CE3 B:TRP271 3.8 14.8 1.0 O B:HOH548 4.0 17.9 1.0 CE1 B:HIS319 4.2 15.5 1.0 O B:HIS320 4.2 13.7 1.0 C B:ALA270 4.3 14.9 1.0 O B:PRO178 4.3 15.3 1.0 CD2 B:HIS319 4.3 15.4 1.0 CB B:ALA179 4.4 15.6 1.0 C B:ALA269 4.4 14.4 1.0 CZ3 B:TRP271 4.4 14.6 1.0 O B:ALA269 4.5 14.0 1.0 CA B:ALA269 4.5 14.6 1.0 O B:HOH506 4.5 16.9 1.0 N B:ALA270 4.8 14.2 1.0 CB B:TRP271 4.8 14.4 1.0 CD2 B:TRP271 4.8 14.5 1.0 CB B:ALA269 4.9 15.1 1.0 O B:ASP177 5.0 15.2 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, 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, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:27.8 occ:1.00 O B:HOH605 2.4 26.0 1.0 O A:HOH667 2.4 39.3 1.0 OG1 B:THR363 2.5 19.5 1.0 O B:HOH721 2.5 29.5 1.0 O A:HOH684 2.6 23.9 1.0 O B:HOH758 3.7 48.4 1.0 CB B:THR363 3.7 19.7 1.0 O B:HOH776 4.0 33.9 1.0 N B:THR363 4.1 20.7 1.0 O B:VAL308 4.1 17.9 1.0 O B:ILE361 4.2 21.1 1.0 O B:HOH505 4.2 26.9 1.0 O A:HOH723 4.2 27.0 1.0 CA B:THR363 4.4 19.8 1.0 OD1 A:ASP263 4.5 21.0 1.0 OD2 A:ASP263 4.6 22.3 1.0 N B:VAL308 4.7 18.4 1.0 CG2 B:THR363 4.8 19.4 1.0 CG A:ASP263 5.0 20.7 1.0 C B:GLU362 5.0 21.8 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