Sodium in PDB 5glk: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form.

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form., PDB code: 5glk 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)	78.87 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.483, 61.327, 79.226, 90.00, 95.44, 90.00
R / Rfree (%)	15.8 / 18.6

The binding sites of Sodium atom in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form. (pdb code 5glk). 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 Compost Microbial Metagenome, Calcium-Free Form., PDB code: 5glk:
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 Compost Microbial Metagenome, 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 Compost Microbial Metagenome, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:13.8 occ:1.00 O A:HOH514 2.2 14.6 1.0 O A:HOH629 2.3 8.8 1.0 O A:HOH704 2.3 9.2 1.0 O A:HOH561 2.3 7.2 1.0 O A:HOH582 2.4 11.7 1.0 O A:ALA270 3.5 7.2 1.0 NE2 A:HIS319 3.5 9.1 1.0 OG A:SER59 3.8 8.4 1.0 O A:HOH537 3.9 10.8 1.0 CE3 A:TRP271 3.9 7.0 1.0 O A:HIS320 4.1 7.3 1.0 CD2 A:HIS319 4.2 9.0 1.0 O A:PRO178 4.3 7.3 1.0 O A:HOH509 4.4 12.1 1.0 C A:ALA269 4.4 7.0 1.0 O A:ALA269 4.5 6.7 1.0 CA A:ALA269 4.5 7.2 1.0 C A:ALA270 4.5 7.1 1.0 CZ3 A:TRP271 4.5 7.0 1.0 CB A:ALA179 4.5 7.7 1.0 CE1 A:HIS319 4.6 9.0 1.0 CB A:ALA269 4.8 7.2 1.0 CB A:TRP271 4.8 6.8 1.0 CD2 A:TRP271 4.9 6.9 1.0 N A:ALA270 4.9 6.9 1.0 O A:ASP177 5.0 8.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, 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 Compost Microbial Metagenome, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:27.3 occ:1.00 O A:HOH553 2.3 16.0 1.0 O B:HOH602 2.4 14.2 1.0 O B:HOH639 2.4 31.0 1.0 O A:HOH759 2.4 26.6 1.0 OG1 A:THR363 2.4 9.5 1.0 O A:HOH588 3.7 25.1 1.0 O A:HOH769 3.7 36.3 1.0 CB A:THR363 3.7 9.6 1.0 O B:HOH579 3.8 19.4 1.0 N A:THR363 4.1 9.7 1.0 O A:VAL308 4.1 8.4 1.0 O A:ILE361 4.2 10.7 1.0 OD2 B:ASP263 4.2 20.0 1.0 OD1 B:ASP263 4.3 18.0 1.0 N A:VAL308 4.4 8.2 1.0 CA A:THR363 4.4 9.5 1.0 CG B:ASP263 4.7 18.1 1.0 CG2 A:THR363 4.8 9.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, 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 Compost Microbial Metagenome, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:16.3 occ:1.00 O B:HOH508 2.3 15.4 1.0 O B:HOH628 2.3 10.4 1.0 O B:HOH541 2.3 12.2 1.0 O B:HOH629 2.3 11.3 1.0 O B:HOH580 2.4 12.0 1.0 O B:ALA270 3.5 10.6 1.0 NE2 B:HIS319 3.5 10.6 1.0 OG B:SER59 3.8 10.0 1.0 CE3 B:TRP271 3.9 10.1 1.0 O B:HOH545 4.0 13.8 1.0 O B:HIS320 4.1 9.4 1.0 CD2 B:HIS319 4.2 10.6 1.0 O B:PRO178 4.3 10.4 1.0 CB B:ALA179 4.4 10.6 1.0 C B:ALA269 4.4 9.9 1.0 CA B:ALA269 4.5 10.1 1.0 CZ3 B:TRP271 4.5 9.9 1.0 O B:HOH504 4.5 14.1 1.0 CE1 B:HIS319 4.5 10.6 1.0 C B:ALA270 4.5 10.3 1.0 O B:ALA269 4.5 9.8 1.0 CB B:ALA269 4.8 10.2 1.0 CB B:TRP271 4.9 10.1 1.0 N B:ALA270 4.9 9.8 1.0 CD2 B:TRP271 4.9 9.9 1.0 O B:ASP177 5.0 10.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, 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 Compost Microbial Metagenome, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:22.3 occ:1.00 O B:HOH538 2.3 17.8 1.0 O B:HOH693 2.4 23.6 1.0 O A:HOH583 2.4 29.2 1.0 OG1 B:THR363 2.5 15.2 1.0 O B:HOH662 2.6 16.5 1.0 O B:HOH756 2.6 41.2 1.0 CB B:THR363 3.7 15.3 1.0 O B:HOH750 3.9 29.2 1.0 O B:HOH514 3.9 23.7 1.0 N B:THR363 4.0 16.0 1.0 O B:ILE361 4.1 16.9 1.0 O B:VAL308 4.1 12.0 1.0 O A:HOH646 4.3 17.4 1.0 CA B:THR363 4.4 15.2 1.0 OD1 A:ASP263 4.5 13.9 1.0 OD2 A:ASP263 4.5 14.6 1.0 N B:VAL308 4.7 12.2 1.0 CG2 B:THR363 4.9 14.9 1.0 O A:HOH787 4.9 29.8 1.0 C B:GLU362 4.9 17.6 1.0 CG A:ASP263 5.0 13.1 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