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Sodium in PDB 5glk: Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form.

Protein crystallography data

The structure of Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form., PDB code: 5glk 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) 78.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.483, 61.327, 79.226, 90.00, 95.44, 90.00
R / Rfree (%) 15.8 / 18.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, Calcium-Free Form. (pdb code 5glk). 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 Compost Microbial Metagenome, Calcium-Free Form., PDB code: 5glk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5glk

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

b:13.8
occ:1.00
O A:HOH514 2.2 14.6 1.0
O A:HOH629 2.3 8.8 1.0
O A:HOH704 2.3 9.2 1.0
O A:HOH561 2.3 7.2 1.0
O A:HOH582 2.4 11.7 1.0
O A:ALA270 3.5 7.2 1.0
NE2 A:HIS319 3.5 9.1 1.0
OG A:SER59 3.8 8.4 1.0
O A:HOH537 3.9 10.8 1.0
CE3 A:TRP271 3.9 7.0 1.0
O A:HIS320 4.1 7.3 1.0
CD2 A:HIS319 4.2 9.0 1.0
O A:PRO178 4.3 7.3 1.0
O A:HOH509 4.4 12.1 1.0
C A:ALA269 4.4 7.0 1.0
O A:ALA269 4.5 6.7 1.0
CA A:ALA269 4.5 7.2 1.0
C A:ALA270 4.5 7.1 1.0
CZ3 A:TRP271 4.5 7.0 1.0
CB A:ALA179 4.5 7.7 1.0
CE1 A:HIS319 4.6 9.0 1.0
CB A:ALA269 4.8 7.2 1.0
CB A:TRP271 4.8 6.8 1.0
CD2 A:TRP271 4.9 6.9 1.0
N A:ALA270 4.9 6.9 1.0
O A:ASP177 5.0 8.0 1.0

Sodium binding site 2 out of 4 in 5glk

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

b:27.3
occ:1.00
O A:HOH553 2.3 16.0 1.0
O B:HOH602 2.4 14.2 1.0
O B:HOH639 2.4 31.0 1.0
O A:HOH759 2.4 26.6 1.0
OG1 A:THR363 2.4 9.5 1.0
O A:HOH588 3.7 25.1 1.0
O A:HOH769 3.7 36.3 1.0
CB A:THR363 3.7 9.6 1.0
O B:HOH579 3.8 19.4 1.0
N A:THR363 4.1 9.7 1.0
O A:VAL308 4.1 8.4 1.0
O A:ILE361 4.2 10.7 1.0
OD2 B:ASP263 4.2 20.0 1.0
OD1 B:ASP263 4.3 18.0 1.0
N A:VAL308 4.4 8.2 1.0
CA A:THR363 4.4 9.5 1.0
CG B:ASP263 4.7 18.1 1.0
CG2 A:THR363 4.8 9.5 1.0

Sodium binding site 3 out of 4 in 5glk

Go back to Sodium Binding Sites List in 5glk
Sodium binding site 3 out of 4 in the Crystal Structure of COXYL43, GH43 Beta-Xylosidase/Alpha- Arabinofuranosidase From A Compost Microbial Metagenome, 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 Compost Microbial Metagenome, Calcium-Free Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:16.3
occ:1.00
O B:HOH508 2.3 15.4 1.0
O B:HOH628 2.3 10.4 1.0
O B:HOH541 2.3 12.2 1.0
O B:HOH629 2.3 11.3 1.0
O B:HOH580 2.4 12.0 1.0
O B:ALA270 3.5 10.6 1.0
NE2 B:HIS319 3.5 10.6 1.0
OG B:SER59 3.8 10.0 1.0
CE3 B:TRP271 3.9 10.1 1.0
O B:HOH545 4.0 13.8 1.0
O B:HIS320 4.1 9.4 1.0
CD2 B:HIS319 4.2 10.6 1.0
O B:PRO178 4.3 10.4 1.0
CB B:ALA179 4.4 10.6 1.0
C B:ALA269 4.4 9.9 1.0
CA B:ALA269 4.5 10.1 1.0
CZ3 B:TRP271 4.5 9.9 1.0
O B:HOH504 4.5 14.1 1.0
CE1 B:HIS319 4.5 10.6 1.0
C B:ALA270 4.5 10.3 1.0
O B:ALA269 4.5 9.8 1.0
CB B:ALA269 4.8 10.2 1.0
CB B:TRP271 4.9 10.1 1.0
N B:ALA270 4.9 9.8 1.0
CD2 B:TRP271 4.9 9.9 1.0
O B:ASP177 5.0 10.2 1.0

Sodium binding site 4 out of 4 in 5glk

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

b:22.3
occ:1.00
O B:HOH538 2.3 17.8 1.0
O B:HOH693 2.4 23.6 1.0
O A:HOH583 2.4 29.2 1.0
OG1 B:THR363 2.5 15.2 1.0
O B:HOH662 2.6 16.5 1.0
O B:HOH756 2.6 41.2 1.0
CB B:THR363 3.7 15.3 1.0
O B:HOH750 3.9 29.2 1.0
O B:HOH514 3.9 23.7 1.0
N B:THR363 4.0 16.0 1.0
O B:ILE361 4.1 16.9 1.0
O B:VAL308 4.1 12.0 1.0
O A:HOH646 4.3 17.4 1.0
CA B:THR363 4.4 15.2 1.0
OD1 A:ASP263 4.5 13.9 1.0
OD2 A:ASP263 4.5 14.6 1.0
N B:VAL308 4.7 12.2 1.0
CG2 B:THR363 4.9 14.9 1.0
O A:HOH787 4.9 29.8 1.0
C B:GLU362 4.9 17.6 1.0
CG A:ASP263 5.0 13.1 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 11:01:42 2020

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