Sodium in PDB 6yyi: Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose

All present enzymatic activity of Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose:
3.2.1.37;

The structure of Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose, PDB code: 6yyi was solved by P.Lafite, R.Daniellou, D.Bretagne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.57 / 2.67
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.950, 160.950, 103.630, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22.7

The binding sites of Sodium atom in the Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose (pdb code 6yyi). 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 Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose, PDB code: 6yyi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose


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 Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na708 b:41.0 occ:1.00 N B:GLU323 3.1 44.3 1.0 N B:ARG27 3.2 46.6 1.0 NE1 B:TRP118 3.4 52.5 1.0 N B:GLU324 3.7 54.5 1.0 CA B:GLY26 3.7 47.5 1.0 CD1 B:LEU30 3.8 43.6 1.0 CG B:GLU324 3.9 52.2 1.0 CA B:GLU323 3.9 50.2 1.0 C B:GLY26 3.9 47.6 1.0 CB B:ARG27 4.0 44.9 1.0 C B:PHE322 4.0 47.3 1.0 CA B:PHE322 4.0 45.7 1.0 CG B:ARG27 4.1 50.9 1.0 C B:GLU323 4.1 52.7 1.0 CD1 B:PHE322 4.1 45.9 1.0 CE2 B:TRP118 4.1 50.5 1.0 CG B:PHE322 4.2 47.5 1.0 CD1 B:TRP118 4.2 54.4 1.0 CA B:ARG27 4.2 44.1 1.0 CB B:GLU323 4.2 50.0 1.0 CE1 B:PHE322 4.3 47.8 1.0 CD2 B:PHE322 4.4 47.2 1.0 CZ2 B:TRP118 4.4 54.1 1.0 CA B:GLU324 4.5 49.5 1.0 NE B:ARG27 4.5 49.6 1.0 CZ B:PHE322 4.5 49.5 1.0 CE2 B:PHE322 4.6 51.7 1.0 CB B:GLU324 4.6 46.9 1.0 CG B:LEU30 4.7 48.5 1.0 CB B:PHE322 4.7 43.4 1.0 CD B:ARG27 4.8 48.8 1.0 CD B:GLU324 4.8 55.2 1.0 OE1 B:GLU324 4.9 52.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose


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 Beta-D-Xylosidase From Dictyoglomus Thermophilum Bound to Beta-D-Xylopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na709 b:61.5 occ:1.00 NH1 B:ARG396 2.7 53.8 1.0 ND2 B:ASN2 3.2 70.2 1.0 CB B:ASN2 3.6 70.6 1.0 CG B:ASN2 3.7 78.0 1.0 CZ B:ARG396 3.9 57.1 1.0 CD B:ARG396 4.0 50.9 1.0 CG B:ARG396 4.0 54.5 1.0 CE1 B:TYR398 4.1 59.2 1.0 OH B:TYR398 4.2 62.7 1.0 CZ B:TYR398 4.3 62.7 1.0 NE B:ARG396 4.4 51.3 1.0 CB B:HIS368 4.7 47.9 1.0 OD1 B:ASN2 4.8 83.6 1.0 CD1 B:TYR398 4.8 59.3 1.0 OD1 B:ASP366 4.9 58.7 1.0 NH2 B:ARG396 4.9 56.5 1.0 CA B:ASN2 5.0 72.8 1.0

D.Bretagne, A.Paris, R.De Vaumas, P.Lafite, R.Daniellou. Crystal Structure of Dictyoglomus Thermophilum Beta-D-Xylosidase Dtxyl Unravels the Structural Determinants For Efficient Notoginsenoside R1 Hydrolysis. Biochimie V. 181 34 2020.
ISSN: ISSN 0300-9084
PubMed: 33242495
DOI: 10.1016/J.BIOCHI.2020.11.017