Sodium in PDB 1od8: Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam

All present enzymatic activity of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam:
3.2.1.8;

The structure of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam, PDB code: 1od8 was solved by T.M.Gloster, S.Roberts, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.814, 45.878, 85.737, 90.00, 90.00, 90.00
R / Rfree (%)	10.3 / 12.6

The binding sites of Sodium atom in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam (pdb code 1od8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam, PDB code: 1od8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1303 b:30.9 occ:1.00 OD2 A:ASP298 1.9 13.0 0.5 O A:HOH2303 2.4 36.2 1.0 CG A:ASP298 2.7 12.0 0.5 O A:THR294 3.0 9.3 1.0 O A:HOH2609 3.1 18.0 1.0 OD1 A:ASP298 3.3 13.7 0.5 O A:HOH2606 3.3 22.9 1.0 CG2 A:THR294 3.3 13.4 1.0 N A:ASP298 3.5 8.1 1.0 CB A:ASP298 3.7 11.0 0.5 C A:THR294 3.7 8.9 1.0 CB A:LEU297 3.7 8.0 1.0 CB A:ASP298 3.8 9.5 0.5 CA A:THR294 3.8 8.9 1.0 CA A:ASP298 3.9 9.0 1.0 CD2 A:LEU297 3.9 11.1 1.0 CG A:LEU297 4.0 8.2 1.0 CB A:THR294 4.1 11.0 1.0 C A:LEU297 4.2 7.8 1.0 O A:HOH2611 4.4 37.2 1.0 O A:HOH2308 4.4 33.5 1.0 CA A:LEU297 4.5 7.3 1.0 O A:HOH2009 4.5 20.0 0.4 OG1 A:THR294 4.7 15.1 1.0 CG A:ASP298 4.9 12.8 0.5 O A:HOH2612 4.9 33.5 0.6 N A:LEU297 4.9 6.9 1.0 O A:LEU297 4.9 8.3 1.0 N A:ALA295 5.0 8.2 1.0

Sodium binding site 2 out of 4 in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1304 b:49.3 occ:1.00 O A:GLY302 1.9 26.4 1.0 C A:GLY302 2.8 20.7 1.0 N A:GLY303 3.1 26.9 1.0 OD1 A:ASP298 3.2 17.6 0.5 O A:ASP298 3.8 9.9 1.0 CG A:ASP298 3.9 12.8 0.5 O A:HOH2611 4.0 37.2 1.0 OD2 A:ASP298 4.1 16.5 0.5 CA A:GLY302 4.2 14.8 1.0 O A:HOH2617 4.2 39.5 1.0 N A:GLY302 4.4 11.4 1.0 O A:ASN301 4.5 15.5 1.0 C A:ASN301 4.6 11.5 1.0 C A:ASP298 4.7 9.0 1.0 CB A:ASP298 5.0 9.5 0.5

Sodium binding site 3 out of 4 in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1305 b:34.7 occ:1.00 OE1 A:GLU2 2.1 24.8 1.0 O A:HOH2014 2.8 20.6 1.0 N A:SER3 2.8 11.0 1.0 CB A:GLU2 3.0 11.7 1.0 CD A:GLU2 3.1 19.6 1.0 CA A:GLU2 3.1 11.0 1.0 C A:GLU2 3.4 11.0 1.0 CG A:GLU2 3.5 18.6 1.0 OG A:SER3 3.5 23.7 1.0 CA A:SER3 4.0 11.0 1.0 CB A:ALA7 4.0 9.4 1.0 CB A:SER3 4.1 16.3 1.0 OE2 A:GLU2 4.1 27.5 1.0 N A:THR4 4.3 8.6 1.0 N A:GLU2 4.5 13.1 1.0 C A:SER3 4.6 9.5 1.0 O A:GLU2 4.7 13.3 1.0 OG1 A:THR4 4.7 11.5 1.0

Sodium binding site 4 out of 4 in the Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xylanase XYN10A From Streptomyces Lividans in Complex with Xylobio-Isofagomine Lactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1312 b:36.7 occ:1.00 O A:HOH2102 2.7 21.1 1.0 O A:HOH2014 3.3 20.6 1.0 CG2 A:THR4 3.7 12.4 1.0 O A:HOH2042 4.1 20.0 0.8 CG A:ARG36 4.3 13.0 1.0 O A:HOH2040 4.5 14.4 0.2 OG1 A:THR4 4.6 11.5 1.0 O A:ARG36 4.6 9.1 1.0 OG A:SER3 4.7 23.7 1.0 CB A:THR4 4.8 9.9 1.0

T.M.Gloster, S.J.Williams, C.Tarling, S.Roberts, C.Dupont, P.Jodoin, F.Shareck, S.G.Withers, G.J.Davies. A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds As Its Amide Tautomer Chem.Commun.(Camb.) V. 8 944 2003.
ISSN: ISSN 1359-7345
PubMed: 12744311
DOI: 10.1039/B301829F