Calcium in PDB 5gll: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome, Calcium-Bound Form

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome, Calcium-Bound Form, PDB code: 5gll 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)	78.59 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.490, 60.935, 78.901, 90.00, 95.05, 90.00
R / Rfree (%)	15.8 / 18.5

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome, 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, Calcium-Bound Form (pdb code 5gll). 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, Calcium-Bound Form, PDB code: 5gll:
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, 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, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.7 occ:1.00 O A:HOH641 2.4 12.4 1.0 O A:HOH575 2.4 9.6 1.0 O A:HOH580 2.4 11.3 1.0 O A:HOH571 2.5 12.2 1.0 O A:HOH567 2.5 14.3 1.0 O A:HOH634 2.5 10.6 1.0 NE2 A:HIS319 2.6 12.6 1.0 CD2 A:HIS319 3.5 12.2 1.0 CE1 A:HIS319 3.7 12.4 1.0 OG A:SER59 3.8 12.5 1.0 O A:PRO178 4.1 12.6 1.0 O A:HIS320 4.3 12.0 1.0 O A:PRO127 4.3 14.1 1.0 O A:ALA270 4.3 11.9 1.0 CB A:ALA126 4.4 13.9 1.0 CA A:ALA269 4.6 12.0 1.0 CG A:HIS319 4.7 12.1 1.0 O A:ASP57 4.7 13.1 1.0 ND1 A:HIS319 4.8 12.2 1.0 CE3 A:TRP271 4.8 12.6 1.0 O A:ASP177 4.8 12.7 1.0 C A:ALA269 4.9 12.0 1.0 CB A:ASP177 4.9 12.8 1.0 CB A:ALA269 4.9 12.0 1.0 O A:ALA269 4.9 12.1 1.0 C A:ASP177 5.0 12.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome, 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, Calcium-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:15.4 occ:1.00 O B:HOH607 2.3 12.2 1.0 O B:HOH636 2.4 14.3 1.0 O B:HOH521 2.5 13.8 1.0 O B:HOH549 2.5 12.2 1.0 O B:HOH641 2.5 15.1 1.0 O B:HOH584 2.5 12.8 1.0 NE2 B:HIS319 2.6 14.9 1.0 CD2 B:HIS319 3.4 14.9 1.0 CE1 B:HIS319 3.7 15.1 1.0 OG B:SER59 3.9 14.9 1.0 O B:PRO178 4.1 15.6 1.0 O B:PRO127 4.3 14.5 1.0 CB B:ALA126 4.3 15.8 1.0 O B:ALA270 4.3 15.4 1.0 O B:HIS320 4.3 15.4 1.0 CA B:ALA269 4.6 14.1 1.0 CG B:HIS319 4.7 14.8 1.0 ND1 B:HIS319 4.7 14.6 1.0 O B:ASP57 4.8 13.4 1.0 CE3 B:TRP271 4.8 14.7 1.0 C B:ALA269 4.9 14.2 1.0 O B:ASP177 4.9 15.4 1.0 CB B:ALA269 4.9 14.1 1.0 CB B:ASP177 5.0 15.3 1.0 O B:ALA269 5.0 13.7 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