Atomistry » Sodium » PDB 5g3g-5gwa » 5glo
Atomistry »
  Sodium »
    PDB 5g3g-5gwa »
      5glo »

Sodium in PDB 5glo: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free 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-Free Form, PDB code: 5glo 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) 78.89 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.764, 61.385, 79.239, 90.00, 95.41, 90.00
R / Rfree (%) 15.5 / 17.5

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-Free Form (pdb code 5glo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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-Free Form, PDB code: 5glo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5glo

Go back to Sodium Binding Sites List in 5glo
Sodium binding site 1 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free 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-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:18.8
occ:1.00
O A:HOH682 2.3 16.6 1.0
O A:HOH734 2.3 14.1 1.0
O A:HOH615 2.4 13.6 1.0
O A:HOH533 2.4 15.1 1.0
O A:HOH501 2.4 21.3 1.0
O A:ALA270 3.2 11.9 1.0
NE2 A:HIS319 3.5 14.5 1.0
OG A:SER59 3.8 13.0 1.0
CE3 A:TRP271 3.8 11.6 1.0
O A:HOH534 4.0 14.2 1.0
O A:HIS320 4.2 13.7 1.0
C A:ALA270 4.2 12.1 1.0
CE1 A:HIS319 4.3 14.5 1.0
CD2 A:HIS319 4.3 14.6 1.0
O A:PRO178 4.3 12.3 1.0
C A:ALA269 4.4 12.4 1.0
CB A:ALA179 4.4 12.8 1.0
CZ3 A:TRP271 4.4 11.5 1.0
O A:ALA269 4.5 12.5 1.0
CA A:ALA269 4.5 12.7 1.0
O A:HOH504 4.5 15.1 1.0
CB A:TRP271 4.7 11.6 1.0
N A:ALA270 4.8 12.1 1.0
CD2 A:TRP271 4.8 11.4 1.0
CB A:ALA269 4.9 12.6 1.0
CA A:TRP271 4.9 11.6 1.0
N A:TRP271 5.0 11.8 1.0
O A:ASP177 5.0 13.4 1.0

Sodium binding site 2 out of 4 in 5glo

Go back to Sodium Binding Sites List in 5glo
Sodium binding site 2 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free 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-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:32.0
occ:1.00
O B:HOH544 2.3 32.9 1.0
O B:HOH801 2.4 46.2 1.0
OG1 A:THR363 2.4 14.7 1.0
O B:HOH546 2.4 18.6 1.0
O A:HOH594 2.5 19.4 1.0
O A:HOH775 2.5 30.4 1.0
CB A:THR363 3.7 14.9 1.0
O A:HOH747 3.7 43.3 1.0
O A:HOH824 3.9 44.8 1.0
O A:HOH507 4.1 28.6 1.0
O A:VAL308 4.1 14.1 1.0
O B:HOH610 4.1 25.0 1.0
N A:THR363 4.1 14.9 1.0
O A:ILE361 4.2 15.7 1.0
OD1 B:ASP263 4.3 26.0 1.0
OD2 B:ASP263 4.3 26.3 1.0
N A:VAL308 4.4 13.6 1.0
CA A:THR363 4.4 14.7 1.0
CG2 A:THR363 4.7 14.9 1.0
CG B:ASP263 4.7 25.4 1.0
C A:VAL308 5.0 14.0 1.0

Sodium binding site 3 out of 4 in 5glo

Go back to Sodium Binding Sites List in 5glo
Sodium binding site 3 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:21.5
occ:1.00
O B:HOH612 2.2 17.9 1.0
O B:HOH669 2.3 14.7 1.0
O B:HOH579 2.4 18.0 1.0
O B:HOH613 2.4 14.4 1.0
O B:HOH510 2.4 21.3 1.0
O B:ALA270 3.2 15.7 1.0
NE2 B:HIS319 3.4 15.7 1.0
OG B:SER59 3.7 15.6 1.0
CE3 B:TRP271 3.8 14.8 1.0
O B:HOH548 4.0 17.9 1.0
CE1 B:HIS319 4.2 15.5 1.0
O B:HIS320 4.2 13.7 1.0
C B:ALA270 4.3 14.9 1.0
O B:PRO178 4.3 15.3 1.0
CD2 B:HIS319 4.3 15.4 1.0
CB B:ALA179 4.4 15.6 1.0
C B:ALA269 4.4 14.4 1.0
CZ3 B:TRP271 4.4 14.6 1.0
O B:ALA269 4.5 14.0 1.0
CA B:ALA269 4.5 14.6 1.0
O B:HOH506 4.5 16.9 1.0
N B:ALA270 4.8 14.2 1.0
CB B:TRP271 4.8 14.4 1.0
CD2 B:TRP271 4.8 14.5 1.0
CB B:ALA269 4.9 15.1 1.0
O B:ASP177 5.0 15.2 1.0

Sodium binding site 4 out of 4 in 5glo

Go back to Sodium Binding Sites List in 5glo
Sodium binding site 4 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compostmicrobial Metagenome in Complex with L-Arabinose, Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:27.8
occ:1.00
O B:HOH605 2.4 26.0 1.0
O A:HOH667 2.4 39.3 1.0
OG1 B:THR363 2.5 19.5 1.0
O B:HOH721 2.5 29.5 1.0
O A:HOH684 2.6 23.9 1.0
O B:HOH758 3.7 48.4 1.0
CB B:THR363 3.7 19.7 1.0
O B:HOH776 4.0 33.9 1.0
N B:THR363 4.1 20.7 1.0
O B:VAL308 4.1 17.9 1.0
O B:ILE361 4.2 21.1 1.0
O B:HOH505 4.2 26.9 1.0
O A:HOH723 4.2 27.0 1.0
CA B:THR363 4.4 19.8 1.0
OD1 A:ASP263 4.5 21.0 1.0
OD2 A:ASP263 4.6 22.3 1.0
N B:VAL308 4.7 18.4 1.0
CG2 B:THR363 4.8 19.4 1.0
CG A:ASP263 5.0 20.7 1.0
C B:GLU362 5.0 21.8 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: Mon Oct 7 21:13:29 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy