Sodium in PDB 2yfo: Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose

All present enzymatic activity of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose:
3.2.1.22;

The structure of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose, PDB code: 2yfo was solved by G.Sulzenbacher, L.Bruel, M.Tison-Cervera, A.Pujol, C.Nicoletti, J.Perrier, A.Galinier, D.Ropartz, M.Fons, F.Pompeo, T.Giardina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.97 / 1.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.016, 111.603, 155.290, 90.00, 90.00, 90.00
R / Rfree (%)	12.436 / 14.171

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Sodium atom in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose (pdb code 2yfo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 27 binding sites of Sodium where determined in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose, PDB code: 2yfo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1728 b:13.8 occ:1.00 OG1 A:THR269 2.7 7.4 1.0 O A:ASN267 2.8 8.1 1.0 O A:GLY188 2.8 8.4 1.0 N A:THR269 3.2 5.3 1.0 N A:GLY188 3.3 7.7 1.0 C A:GLN187 3.3 9.2 1.0 NZ A:LYS263 3.3 18.8 0.4 C A:GLN268 3.4 5.3 1.0 O A:HOH2511 3.4 14.4 1.0 CA A:GLN268 3.5 4.8 1.0 CB A:THR269 3.5 6.0 1.0 C A:GLY188 3.7 8.7 1.0 C A:ASN267 3.7 7.0 1.0 O A:GLN187 3.7 9.0 1.0 CA A:GLN187 3.7 9.7 0.4 O A:HOH2509 3.9 16.4 1.0 CA A:GLN187 3.9 9.8 0.6 CA A:GLY188 3.9 8.7 1.0 CA A:THR269 4.0 5.7 1.0 CE2 A:PHE190 4.0 9.4 1.0 O A:PHE185 4.0 8.0 1.0 N A:GLN268 4.0 5.7 1.0 N A:GLN187 4.1 8.2 1.0 O A:GLN268 4.1 6.4 1.0 CD A:LYS263 4.2 11.7 0.4 CE A:LYS263 4.3 14.1 0.4 CD2 A:PHE190 4.4 7.0 1.0 CB A:PHE185 4.4 6.7 1.0 C A:VAL186 4.6 9.0 1.0 C A:PHE185 4.7 6.9 1.0 CB A:GLN268 4.8 4.9 1.0 O A:VAL186 4.9 11.1 1.0 CG2 A:THR269 4.9 7.0 1.0 N A:GLU189 4.9 8.4 1.0 O A:HOH2506 4.9 19.7 1.0 CA A:ASN267 5.0 6.8 1.0

Sodium binding site 2 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1729 b:12.5 occ:1.00 OE1 A:GLN75 2.7 7.7 1.0 OG1 A:THR82 2.8 7.8 1.0 OD2 A:ASP84 2.9 6.6 1.0 N A:SER79 3.1 6.7 1.0 CB A:ASP84 3.2 5.5 1.0 CB A:PRO78 3.4 6.5 1.0 CA A:PRO78 3.4 6.4 1.0 O A:SER79 3.4 7.6 1.0 CG A:ASP84 3.5 6.3 1.0 CD A:GLN75 3.6 7.4 1.0 CG2 A:THR82 3.7 8.7 1.0 C A:PRO78 3.7 6.7 1.0 CB A:THR82 3.7 8.0 1.0 NE2 A:GLN75 3.7 7.3 1.0 CA A:SER79 4.2 7.4 1.0 C A:SER79 4.2 7.2 1.0 O A:HOH2171 4.4 9.4 1.0 CB A:LEU70 4.4 8.1 1.0 O A:LEU70 4.4 6.2 1.0 CG2 A:ILE88 4.4 8.0 1.0 OG A:SER79 4.6 8.4 1.0 CA A:ASP84 4.6 6.2 1.0 O A:HOH2178 4.7 6.8 1.0 N A:PRO78 4.8 6.4 1.0 OD1 A:ASP84 4.8 6.6 1.0 CG A:PRO78 4.8 5.8 1.0 O A:HOH2175 4.8 16.1 1.0 N A:ASP84 4.9 6.3 1.0 O A:PRO78 4.9 6.8 1.0 CG A:GLN75 5.0 6.0 1.0

Sodium binding site 3 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1730 b:14.6 occ:1.00 OH A:TYR253 2.7 8.2 1.0 O A:TYR493 2.8 7.4 1.0 CD2 A:TYR493 3.3 7.9 1.0 CE1 A:TYR253 3.4 6.9 1.0 CE2 A:TYR493 3.4 8.5 1.0 CZ A:TYR253 3.4 6.9 1.0 CG A:TYR493 3.4 7.8 1.0 C A:TYR493 3.6 6.7 1.0 CB A:VAL496 3.6 7.6 1.0 CZ A:TYR493 3.6 7.9 1.0 N A:LEU497 3.6 7.9 1.0 CD1 A:TYR493 3.7 7.8 1.0 CE1 A:TYR493 3.7 8.2 1.0 CA A:TYR493 3.8 6.8 1.0 CG1 A:VAL496 3.8 8.6 1.0 CD2 A:LEU497 3.9 10.7 1.0 CG A:LEU497 3.9 10.6 1.0 CD2 A:LEU120 4.1 9.8 1.0 C A:VAL496 4.1 7.5 1.0 CB A:TYR493 4.2 6.8 1.0 CA A:VAL496 4.3 7.4 1.0 CA A:LEU497 4.4 8.4 1.0 OH A:TYR493 4.5 9.7 1.0 CB A:LEU497 4.6 9.6 1.0 CD1 A:TYR253 4.6 6.8 1.0 N A:VAL496 4.7 7.9 1.0 CE2 A:TYR253 4.8 6.7 1.0 CG2 A:VAL496 4.8 8.2 1.0 N A:ASP494 4.8 6.8 1.0 O A:VAL496 4.9 7.5 1.0 O A:SER492 5.0 8.7 1.0

Sodium binding site 4 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1731 b:11.7 occ:1.00 O A:HIS226 2.7 6.0 1.0 O A:PHE195 2.9 5.7 1.0 NA A:NA1750 2.9 11.9 1.0 N A:ARG203 3.0 6.4 1.0 CG A:ARG203 3.4 6.4 1.0 C A:TYR196 3.5 5.2 1.0 CA A:ARG203 3.5 6.4 1.0 C A:PHE195 3.5 5.0 1.0 N A:GLY197 3.6 5.3 1.0 C A:HIS226 3.6 5.5 1.0 CA A:TYR196 3.7 5.2 1.0 N A:ASN229 3.8 5.6 1.0 N A:TYR196 3.8 5.0 1.0 C A:GLN227 3.9 5.2 1.0 O A:GLN227 3.9 5.1 1.0 O A:TYR196 3.9 5.9 1.0 N A:TYR228 4.0 5.0 1.0 CB A:ARG203 4.1 6.4 1.0 CA A:TYR228 4.1 5.5 1.0 C A:GLU202 4.1 5.8 1.0 C A:TYR228 4.2 5.7 1.0 CA A:GLU202 4.2 5.1 1.0 CA A:GLY197 4.3 5.6 1.0 N A:GLN227 4.4 5.5 1.0 CB A:GLU202 4.4 6.5 1.0 CB A:ASN229 4.4 5.1 1.0 CA A:GLN227 4.5 5.5 1.0 CA A:ASN229 4.6 5.3 1.0 CA A:HIS226 4.6 5.2 1.0 CD A:ARG203 4.6 5.9 1.0 CA A:PHE195 4.7 5.3 1.0 O A:SER225 4.7 5.9 1.0 CB A:PHE195 4.8 5.5 1.0 C A:ARG203 4.8 6.3 1.0 NH1 A:ARG203 4.8 6.8 1.0

Sodium binding site 5 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1732 b:12.6 occ:1.00 NA A:NA1751 2.8 13.8 1.0 N A:ARG524 2.8 6.3 1.0 O A:GLY521 2.8 6.5 1.0 C A:ARG524 3.2 6.7 1.0 N A:GLY523 3.2 5.9 1.0 CG2 A:ILE536 3.3 6.7 1.0 C A:GLY522 3.4 6.7 1.0 CA A:GLY522 3.4 6.6 1.0 O A:ARG524 3.4 7.0 1.0 N A:SER519 3.4 6.5 1.0 CA A:ARG524 3.5 6.1 1.0 N A:PHE525 3.5 5.6 1.0 CB A:SER519 3.8 6.3 1.0 C A:GLY521 3.8 6.1 1.0 C A:CYS518 3.8 6.4 1.0 C A:GLY523 3.9 5.2 1.0 CB A:ARG524 3.9 7.8 1.0 CA A:CYS518 4.0 6.2 1.0 N A:GLY522 4.0 6.8 1.0 CA A:GLY523 4.1 5.8 1.0 O A:GLY522 4.2 7.2 1.0 CA A:PHE525 4.2 6.5 1.0 CA A:SER519 4.2 6.3 1.0 N A:CYS518 4.4 6.5 1.0 O A:TRP537 4.4 6.8 1.0 O A:SER519 4.5 6.3 1.0 CB A:PHE525 4.5 6.0 1.0 O A:CYS518 4.5 7.0 1.0 O A:HOH2815 4.6 7.5 1.0 C A:SER519 4.7 7.2 1.0 CB A:ILE536 4.7 5.9 1.0 C A:GLY517 4.8 6.2 1.0 O A:GLY517 4.9 6.8 1.0 CG A:ARG524 4.9 7.5 1.0

Sodium binding site 6 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1733 b:14.1 occ:1.00 O A:HOH2367 2.8 8.0 1.0 NH1 A:ARG86 3.0 6.8 1.0 O A:ALA72 3.1 6.8 1.0 OE1 A:GLN268 3.2 9.2 1.0 CA A:PRO74 3.2 5.5 1.0 N A:PRO74 3.3 5.6 1.0 CD A:GLN268 3.4 7.4 1.0 NE2 A:GLN268 3.5 6.9 1.0 C A:LEU73 3.5 5.5 1.0 CB A:PRO74 3.5 5.8 1.0 O A:LEU73 3.7 5.8 1.0 CD A:PRO74 3.8 6.0 1.0 CG A:ASP184 4.0 6.9 1.0 CZ A:ARG86 4.1 5.6 1.0 CB A:ASP184 4.1 7.7 1.0 C A:ALA72 4.1 5.5 1.0 OD2 A:ASP184 4.2 6.6 1.0 OD1 A:ASP184 4.2 9.3 1.0 CG A:PRO74 4.2 5.9 1.0 NH2 A:ARG86 4.3 6.3 1.0 O A:HOH2500 4.3 8.5 1.0 CB A:GLN268 4.3 4.9 1.0 CA A:LEU73 4.3 6.2 1.0 CG A:GLN268 4.4 5.6 1.0 CG1 A:VAL186 4.5 8.8 1.0 O A:PHE185 4.6 8.0 1.0 N A:LEU73 4.6 6.2 1.0 C A:PRO74 4.7 6.0 1.0 O A:HOH2166 4.9 11.5 1.0 C A:PHE185 4.9 6.9 1.0 CA A:VAL186 5.0 7.0 1.0

Sodium binding site 7 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1734 b:14.0 occ:1.00 NA A:NA1752 2.8 15.4 1.0 N A:GLY57 2.8 7.0 1.0 O A:GLY83 2.8 7.4 1.0 CA A:GLY57 3.2 6.8 1.0 CE2 A:TYR85 3.5 7.4 1.0 C A:GLY57 3.5 6.9 1.0 C A:GLY83 3.5 7.5 1.0 O A:GLY57 3.6 6.8 1.0 CA A:GLY83 3.6 6.7 1.0 C A:SER56 3.9 6.4 1.0 OH A:TYR85 4.1 7.7 1.0 CZ A:TYR85 4.2 7.3 1.0 CD2 A:TYR85 4.2 6.8 1.0 O A:PHE55 4.3 6.9 1.0 CA A:SER56 4.3 5.9 1.0 OG A:SER69 4.4 6.5 1.0 O A:HOH2132 4.4 8.2 1.0 N A:ASN58 4.4 6.8 1.0 CB A:ASP71 4.5 6.4 1.0 N A:ASP84 4.8 6.3 1.0 O A:SER56 5.0 7.1 1.0

Sodium binding site 8 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1735 b:13.6 occ:1.00 O A:GLN75 2.8 6.9 1.0 O A:CYS182 2.8 7.0 1.0 N A:ASP184 3.0 6.1 1.0 CG A:HIS33 3.1 6.0 1.0 CB A:HIS33 3.1 6.4 1.0 CA A:LEU183 3.4 6.5 1.0 C A:CYS182 3.5 6.9 1.0 ND1 A:HIS33 3.5 7.0 1.0 C A:GLN75 3.6 6.7 1.0 CD2 A:HIS33 3.6 6.6 1.0 C A:LEU183 3.6 6.0 1.0 N A:LEU183 3.8 6.1 1.0 CB A:ASP184 3.9 7.7 1.0 CA A:GLU76 3.9 5.9 1.0 CA A:ASP184 4.0 6.7 1.0 N A:GLU76 4.1 6.5 1.0 CE1 A:HIS33 4.2 8.2 1.0 NE2 A:HIS33 4.2 7.1 1.0 SG A:CYS182 4.2 7.6 1.0 OE2 A:GLU76 4.3 7.8 1.0 CD A:GLU76 4.4 6.7 1.0 CB A:CYS182 4.4 7.1 1.0 O A:GLU76 4.5 6.9 1.0 OH A:TYR21 4.5 7.5 1.0 OE1 A:GLU76 4.5 7.6 1.0 CG A:ASP184 4.5 6.9 1.0 C A:GLU76 4.5 6.1 1.0 CD2 A:LEU183 4.6 8.3 1.0 CA A:CYS182 4.6 6.3 1.0 CA A:HIS33 4.6 6.9 1.0 N A:GLN75 4.6 5.7 1.0 O A:ASP184 4.7 9.8 1.0 CB A:LEU183 4.7 7.3 1.0 CA A:GLN75 4.7 6.3 1.0 O A:HOH2041 4.7 15.4 1.0 OD2 A:ASP184 4.7 6.6 1.0 O A:LEU183 4.8 6.3 1.0 C A:ASP184 4.8 7.2 1.0 NH1 A:ARG161 4.9 7.9 1.0

Sodium binding site 9 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1736 b:14.3 occ:1.00 O A:GLY211 2.8 7.1 1.0 C A:GLY213 3.4 5.2 1.0 O A:GLY213 3.5 6.5 1.0 N A:THR214 3.5 5.1 1.0 C A:THR214 3.5 5.7 1.0 O A:THR214 3.6 7.2 1.0 C A:GLY211 3.6 6.0 1.0 O A:HIS212 3.6 6.7 1.0 CG1 A:ILE215 3.8 6.2 1.0 N A:ILE215 3.9 4.8 1.0 CD1 A:LEU210 3.9 7.9 1.0 C A:HIS212 3.9 6.1 1.0 CA A:GLY213 3.9 5.7 1.0 N A:GLY211 3.9 6.4 1.0 CA A:THR214 4.0 5.7 1.0 N A:GLY213 4.1 5.5 1.0 CA A:GLY211 4.1 7.2 1.0 N A:HIS212 4.5 5.8 1.0 CD1 A:ILE215 4.5 7.5 1.0 CA A:ILE215 4.6 5.0 1.0 CA A:HIS212 4.7 5.9 1.0 C A:LEU210 4.8 7.2 1.0 CB A:ILE215 4.8 5.0 1.0 CG A:LEU210 4.9 6.1 1.0

Sodium binding site 10 out of 27 in the Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Galactosidase Domain of Alpha-Galactosidase-Sucrose Kinase, Agask, in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1737 b:12.8 occ:1.00 O A:HOH2437 2.7 6.5 1.0 O A:GLY218 2.7 7.0 1.0 OG A:SER225 2.8 5.8 1.0 CB A:SER225 3.4 6.0 1.0 CB A:GLN227 3.5 5.3 1.0 CB A:SER219 3.6 6.0 1.0 CA A:SER219 3.6 5.7 1.0 CD2 A:TYR228 3.6 7.4 1.0 C A:GLY218 3.7 7.3 1.0 N A:TYR228 3.7 5.0 1.0 OG A:SER219 3.9 6.7 1.0 N A:SER219 4.1 6.3 1.0 CB A:TYR228 4.1 6.1 1.0 OE1 A:GLN227 4.2 6.1 1.0 CA A:GLN227 4.2 5.5 1.0 C A:GLN227 4.2 5.2 1.0 CG A:TYR228 4.3 6.4 1.0 O A:TYR228 4.4 6.3 1.0 CA A:TYR228 4.4 5.5 1.0 N A:GLN227 4.5 5.5 1.0 CD A:ARG221 4.5 6.4 1.0 NE A:ARG221 4.5 6.2 1.0 CE2 A:TYR228 4.6 6.3 1.0 CG A:GLN227 4.6 5.7 1.0 O A:SER224 4.7 6.5 1.0 CD A:GLN227 4.9 6.0 1.0 C A:TYR228 4.9 5.7 1.0 CA A:SER225 4.9 5.8 1.0 C A:SER219 5.0 6.8 1.0

L.Bruel, G.Sulzenbacher, M.Tison-Cervera, A.Pujol, C.Nicoletti, J.Perrier, A.Galinier, D.Ropartz, M.Fons, F.Pompeo, T.Giardina. Agask, A Bifunctional Enzyme From the Human Microbiome Coupling Galactosidase and Kinase Activities J.Biol.Chem. V. 286 40814 2011.
ISSN: ISSN 0021-9258
PubMed: 21931163
DOI: 10.1074/JBC.M111.286039