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

Protein crystallography data

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose and Xylotriose, Calcium-Bound Form, PDB code: 5glr 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) 78.60 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.929, 61.343, 79.001, 90.00, 95.79, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 5glr:

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

Sodium (Na) 2 atoms

Calcium Binding Sites:

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 and Xylotriose, Calcium-Bound Form (pdb code 5glr). 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 and Xylotriose, Calcium-Bound Form, PDB code: 5glr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5glr

Go back to Calcium Binding Sites List in 5glr
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 and Xylotriose, 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 and Xylotriose, Calcium-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:10.6
occ:1.00
O A:HOH550 2.4 8.8 1.0
O A:HOH665 2.4 10.8 1.0
O A:HOH656 2.4 9.9 1.0
O A:HOH617 2.5 8.9 1.0
O A:HOH616 2.5 11.2 1.0
O A:HOH715 2.5 10.2 1.0
NE2 A:HIS319 2.5 10.2 1.0
CD2 A:HIS319 3.5 9.8 1.0
CE1 A:HIS319 3.5 10.1 1.0
OG A:SER59 3.8 10.6 1.0
O A:PRO178 4.1 10.2 1.0
O A:ALA270 4.3 9.0 1.0
O A:PRO127 4.4 11.1 1.0
CB A:ALA126 4.4 10.3 1.0
O A:HIS320 4.4 9.0 1.0
ND1 A:HIS319 4.6 9.9 1.0
CG A:HIS319 4.6 9.7 1.0
CA A:ALA269 4.7 9.4 1.0
O A:ASP57 4.8 10.4 1.0
CE3 A:TRP271 4.8 9.5 1.0
O A:ASP177 4.8 9.8 1.0
C A:ALA269 4.9 9.2 1.0
C A:ASP177 5.0 9.8 1.0
CB A:ASP177 5.0 10.2 1.0
C A:PRO178 5.0 10.0 1.0

Calcium binding site 2 out of 2 in 5glr

Go back to Calcium Binding Sites List in 5glr
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 and Xylotriose, 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 and Xylotriose, Calcium-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:12.6
occ:1.00
O B:HOH606 2.4 10.6 1.0
O B:HOH620 2.4 11.1 1.0
O B:HOH541 2.4 9.9 1.0
O B:HOH558 2.5 11.2 1.0
O B:HOH566 2.5 12.1 1.0
NE2 B:HIS319 2.5 10.8 1.0
O B:HOH650 2.6 11.3 1.0
CD2 B:HIS319 3.5 11.0 1.0
CE1 B:HIS319 3.5 11.0 1.0
OG B:SER59 3.8 11.6 1.0
O B:PRO178 4.0 11.3 1.0
O B:ALA270 4.3 11.2 1.0
O B:PRO127 4.3 12.2 1.0
O B:HIS320 4.4 11.7 1.0
CB B:ALA126 4.4 13.0 1.0
ND1 B:HIS319 4.6 10.8 1.0
CG B:HIS319 4.7 11.0 1.0
CA B:ALA269 4.7 10.5 1.0
CE3 B:TRP271 4.7 11.9 1.0
O B:ASP57 4.8 10.5 1.0
O B:ASP177 4.9 11.7 1.0
C B:ALA269 4.9 10.5 1.0
C B:PRO178 5.0 11.4 1.0
C B:ASP177 5.0 11.5 1.0

Reference:

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
Page generated: Sat Dec 12 05:26:41 2020

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