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

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form., PDB code: 5glm 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)	78.61 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.774, 61.647, 79.006, 90.00, 95.77, 90.00
R / Rfree (%)	14.5 / 16.9

The binding sites of Sodium atom in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form. (pdb code 5glm). 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 in Complex with Xylotriose, Calcium-Free Form., PDB code: 5glm:
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 in Complex with 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 Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:18.4 occ:1.00 O A:HOH1024 2.3 13.7 1.0 O A:HOH1161 2.3 14.0 1.0 O A:HOH1025 2.3 12.6 1.0 O A:HOH1026 2.3 14.9 1.0 O A:HOH1603 2.4 18.0 1.0 O A:ALA270 3.2 11.5 1.0 NE2 A:HIS319 3.4 13.3 1.0 OG A:SER59 3.8 12.8 1.0 CE3 A:TRP271 3.8 11.8 1.0 O A:HOH1023 4.0 14.0 1.0 O A:HIS320 4.1 11.1 1.0 C A:ALA270 4.2 11.4 1.0 CD2 A:HIS319 4.2 13.4 1.0 CE1 A:HIS319 4.2 13.5 1.0 O A:PRO178 4.4 12.0 1.0 C A:ALA269 4.4 11.3 1.0 CB A:ALA179 4.4 12.4 1.0 O A:ALA269 4.4 10.9 1.0 CZ3 A:TRP271 4.5 11.9 1.0 O A:HOH1274 4.5 16.8 1.0 CA A:ALA269 4.6 11.4 1.0 CB A:TRP271 4.7 11.6 1.0 N A:ALA270 4.8 11.1 1.0 CD2 A:TRP271 4.8 11.7 1.0 CA A:TRP271 4.9 11.5 1.0 N A:TRP271 5.0 11.3 1.0 CB A:ALA269 5.0 11.2 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 in Complex with 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 Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:19.1 occ:1.00 OG1 A:THR363 2.3 13.7 1.0 O A:HOH1412 2.4 25.3 1.0 O A:HOH1244 2.4 22.5 1.0 O A:HOH1344 2.5 15.5 1.0 O A:HOH1243 2.5 16.2 1.0 O4B B:XYP511 2.5 26.6 1.0 CB A:THR363 3.6 13.8 1.0 C4B B:XYP511 3.6 27.7 1.0 C5B B:XYP511 3.8 27.9 1.0 O A:HOH1293 3.9 41.0 1.0 O B:HOH1345 4.0 19.8 1.0 O A:HOH1299 4.0 38.0 1.0 O A:HOH1292 4.1 24.1 1.0 C3B B:XYP511 4.1 27.6 1.0 N A:THR363 4.1 14.4 1.0 O A:VAL308 4.1 12.5 1.0 O B:HOH1580 4.2 34.7 1.0 O A:ILE361 4.3 15.9 1.0 OD1 B:ASP263 4.3 18.8 1.0 CA A:THR363 4.4 14.0 1.0 OD2 B:ASP263 4.4 20.4 1.0 N A:VAL308 4.5 12.2 1.0 CG2 A:THR363 4.7 13.6 1.0 O3B B:XYP511 4.7 28.6 1.0 CG B:ASP263 4.8 19.0 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 in Complex with 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 Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na410 b:20.4 occ:1.00 O B:HOH1328 2.2 16.4 1.0 O B:HOH1331 2.3 14.8 1.0 O B:HOH1327 2.3 14.7 1.0 O B:HOH1488 2.4 14.8 1.0 O B:HOH1607 2.4 21.9 1.0 O B:ALA270 3.2 13.3 1.0 NE2 B:HIS319 3.4 14.4 1.0 CE3 B:TRP271 3.8 13.7 1.0 OG B:SER59 3.9 13.7 1.0 O B:HOH1330 4.0 15.5 1.0 CE1 B:HIS319 4.2 14.7 1.0 O B:HIS320 4.2 13.7 1.0 C B:ALA270 4.2 13.2 1.0 CD2 B:HIS319 4.3 14.2 1.0 O B:PRO178 4.3 14.8 1.0 C B:ALA269 4.4 12.4 1.0 CB B:ALA179 4.4 14.6 1.0 O B:ALA269 4.4 12.2 1.0 CA B:ALA269 4.5 12.3 1.0 CZ3 B:TRP271 4.5 13.7 1.0 O B:HOH1489 4.6 17.6 1.0 CB B:TRP271 4.7 13.5 1.0 N B:ALA270 4.8 12.5 1.0 CD2 B:TRP271 4.8 13.5 1.0 CB B:ALA269 4.9 12.5 1.0 CA B:TRP271 5.0 13.7 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 in Complex with 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 Compost Microbial Metagenome in Complex with Xylotriose, Calcium-Free Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na411 b:23.4 occ:1.00 O B:HOH1572 2.4 35.3 1.0 O B:HOH1235 2.4 28.9 1.0 O B:HOH1315 2.4 27.1 1.0 O B:HOH1407 2.4 22.4 1.0 OG1 B:THR363 2.5 17.4 1.0 O B:HOH1153 2.5 19.9 1.0 CB B:THR363 3.7 17.9 1.0 O B:HOH1408 4.0 31.1 1.0 O B:VAL308 4.1 15.0 1.0 N B:THR363 4.2 18.6 1.0 O B:HOH1406 4.2 23.0 1.0 O B:ILE361 4.2 20.5 1.0 O A:HOH1152 4.3 19.3 1.0 OD1 A:ASP263 4.3 16.9 1.0 OD2 A:ASP263 4.4 18.2 1.0 CA B:THR363 4.5 18.0 1.0 O A:HOH1155 4.5 39.4 1.0 N B:VAL308 4.6 15.2 1.0 CG A:ASP263 4.8 16.5 1.0 CG2 B:THR363 4.8 17.4 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