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Sodium 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:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5glp

Go back to Sodium Binding Sites List in 5glp
Sodium 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 Sodium with other atoms in the Na 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:Na402

b:29.4
occ:1.00
O B:HOH594 2.3 16.0 1.0
O B:HOH825 2.3 45.6 1.0
O B:HOH553 2.4 31.6 1.0
OG1 A:THR363 2.4 14.4 1.0
O A:HOH779 2.5 32.0 1.0
O A:HOH581 2.6 17.0 1.0
CB A:THR363 3.7 14.1 1.0
O A:HOH734 3.7 42.8 1.0
O A:HOH831 3.9 39.9 1.0
O A:HOH536 4.0 26.4 1.0
O A:VAL308 4.1 12.9 1.0
O B:HOH604 4.1 24.7 1.0
N A:THR363 4.2 14.2 1.0
O A:ILE361 4.2 15.7 1.0
OD1 B:ASP263 4.3 21.7 1.0
OD2 B:ASP263 4.3 24.2 1.0
CA A:THR363 4.4 13.9 1.0
N A:VAL308 4.5 12.6 1.0
CG B:ASP263 4.7 22.2 1.0
CG2 A:THR363 4.7 14.1 1.0
O B:HOH777 4.8 36.9 1.0

Sodium binding site 2 out of 2 in 5glp

Go back to Sodium Binding Sites List in 5glp
Sodium 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 Sodium with other atoms in the Na 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:Na402

b:24.1
occ:1.00
O B:HOH835 2.3 42.8 1.0
O B:HOH575 2.4 23.5 1.0
OG1 B:THR363 2.5 18.0 1.0
O A:HOH626 2.5 23.6 1.0
O B:HOH737 2.5 23.3 1.0
O A:HOH583 2.5 33.3 1.0
CB B:THR363 3.7 18.4 1.0
O B:HOH738 4.0 36.7 1.0
O B:HOH805 4.0 29.3 1.0
N B:THR363 4.1 19.4 1.0
O B:VAL308 4.1 16.4 1.0
O B:ILE361 4.2 20.8 1.0
O B:HOH502 4.2 24.8 1.0
O A:HOH657 4.3 22.2 1.0
CA B:THR363 4.4 18.9 1.0
OD1 A:ASP263 4.5 18.4 1.0
OD2 A:ASP263 4.5 19.9 1.0
N B:VAL308 4.6 16.2 1.0
O A:HOH806 4.6 36.0 1.0
CG2 B:THR363 4.8 18.1 1.0
CG A:ASP263 4.9 18.5 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: Tue Dec 15 11:01:46 2020

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