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

Protein crystallography data

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

Other elements in 5glp:

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

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, 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 5glp

Go back to Calcium Binding Sites List in 5glp
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 5glp

Go back to Calcium Binding Sites List in 5glp
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

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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