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

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Bound Form, PDB code: 5glp 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)	78.71 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.801, 61.329, 79.070, 90.00, 95.51, 90.00
R / Rfree (%)	15.1 / 17.4

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

Sodium

(Na)

2 atoms

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

Calcium 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, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.2 occ:1.00 O A:HOH575 2.4 11.5 1.0 O A:HOH653 2.4 13.2 1.0 O A:HOH640 2.4 11.9 1.0 O A:HOH615 2.5 11.5 1.0 O A:HOH553 2.5 12.4 1.0 O A:HOH697 2.6 12.9 1.0 NE2 A:HIS319 2.6 11.6 1.0 CD2 A:HIS319 3.5 11.7 1.0 CE1 A:HIS319 3.6 11.6 1.0 OG A:SER59 3.8 12.0 1.0 O A:PRO178 4.1 11.7 1.0 O A:ALA270 4.3 10.8 1.0 O A:PRO127 4.3 12.6 1.0 CB A:ALA126 4.4 12.4 1.0 O A:HIS320 4.4 11.7 1.0 CA A:ALA269 4.6 11.3 1.0 O A:ASP57 4.7 12.0 1.0 CG A:HIS319 4.7 11.6 1.0 ND1 A:HIS319 4.7 11.4 1.0 CE3 A:TRP271 4.8 11.7 1.0 C A:ALA269 4.8 11.2 1.0 O A:ASP177 4.9 11.7 1.0 O A:ALA269 5.0 10.8 1.0 C A:ASP177 5.0 11.6 1.0 CB A:ASP177 5.0 11.9 1.0

Calcium 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, Calcium-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:13.0 occ:1.00 O B:HOH636 2.4 13.5 1.0 O B:HOH633 2.4 11.8 1.0 O B:HOH588 2.4 11.1 1.0 O B:HOH514 2.4 13.4 1.0 O B:HOH603 2.5 11.2 1.0 O B:HOH696 2.5 13.5 1.0 NE2 B:HIS319 2.6 12.6 1.0 CD2 B:HIS319 3.5 12.7 1.0 CE1 B:HIS319 3.6 12.7 1.0 OG B:SER59 3.8 13.2 1.0 O B:PRO178 4.1 13.1 1.0 O B:ALA270 4.3 13.5 1.0 O B:HIS320 4.4 12.6 1.0 O B:PRO127 4.4 13.6 1.0 CB B:ALA126 4.4 13.8 1.0 CA B:ALA269 4.7 13.0 1.0 CG B:HIS319 4.7 12.7 1.0 ND1 B:HIS319 4.7 12.4 1.0 O B:ASP57 4.8 12.8 1.0 CE3 B:TRP271 4.8 13.4 1.0 C B:ALA269 4.9 12.9 1.0 O B:ASP177 4.9 12.9 1.0 O B:ALA269 4.9 13.2 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