Sodium in PDB 3ues: Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin

All present enzymatic activity of Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin:
3.2.1.111;

The structure of Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin, PDB code: 3ues was solved by H.Sakurama, S.Fushinobu, E.Yoshida, Y.Honda, M.Hidaka, H.Ashida, M.Kitaoka, T.Katayama, K.Yamamoto, H.Kumagai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.91 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.981, 120.597, 142.469, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.1

The binding sites of Sodium atom in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin (pdb code 3ues). 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 Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin, PDB code: 3ues:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin


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 Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:21.1 occ:1.00 O A:ASN377 2.3 23.4 1.0 O A:HIS372 2.4 22.7 1.0 OG1 A:THR380 2.5 22.6 1.0 O A:THR380 2.5 19.9 1.0 OD1 A:ASP375 2.6 23.8 1.0 O A:SER471 2.7 20.7 1.0 O A:HOH604 3.3 33.0 1.0 C A:THR380 3.3 19.0 1.0 C A:ASN377 3.4 22.8 1.0 C A:HIS372 3.5 23.4 1.0 CG A:ASP375 3.6 27.8 1.0 CB A:THR380 3.6 20.9 1.0 C A:SER471 3.7 18.7 1.0 CA A:THR380 3.8 18.5 1.0 N A:THR380 3.8 20.6 1.0 OD2 A:ASP375 3.8 28.3 1.0 N A:ASN377 3.9 25.7 1.0 CA A:ASN377 4.0 26.0 1.0 CA A:SER471 4.0 20.4 1.0 CA A:HIS372 4.0 21.2 1.0 CB A:ASN377 4.1 24.0 1.0 CB A:HIS372 4.2 23.7 1.0 CB A:SER471 4.3 19.5 1.0 N A:PHE381 4.3 20.0 1.0 N A:ARG378 4.5 24.2 1.0 O A:HOH547 4.5 32.7 1.0 N A:LEU373 4.6 20.8 1.0 CA A:PHE381 4.7 18.2 1.0 CG2 A:THR380 4.8 24.2 1.0 CA A:ARG378 4.8 20.1 1.0 CA A:LEU373 4.9 23.5 1.0 N A:ARG472 4.9 19.1 1.0 N A:ASP375 4.9 24.4 1.0 C A:ARG378 4.9 22.2 1.0 CB A:ASP375 4.9 25.5 1.0 C A:LEU373 4.9 24.2 1.0 N A:GLY376 5.0 28.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin


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 Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis Complexed with Deoxyfuconojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:20.7 occ:1.00 O B:ASN377 2.3 21.8 1.0 O B:HIS372 2.3 21.2 1.0 OG1 B:THR380 2.4 20.5 1.0 O B:THR380 2.5 21.9 1.0 OD1 B:ASP375 2.6 22.9 1.0 O B:SER471 2.7 18.7 1.0 C B:THR380 3.3 19.2 1.0 O B:HOH491 3.3 35.9 1.0 C B:ASN377 3.4 19.8 1.0 C B:HIS372 3.4 20.9 1.0 CB B:THR380 3.6 19.5 1.0 CG B:ASP375 3.6 26.0 1.0 C B:SER471 3.7 16.4 1.0 CA B:THR380 3.8 20.5 1.0 OD2 B:ASP375 3.8 24.6 1.0 N B:THR380 3.9 21.0 1.0 N B:ASN377 3.9 20.8 1.0 CA B:HIS372 4.0 20.9 1.0 CA B:SER471 4.0 17.4 1.0 CA B:ASN377 4.1 20.3 1.0 CB B:ASN377 4.1 24.8 1.0 CB B:SER471 4.2 19.9 1.0 CB B:HIS372 4.2 19.4 1.0 N B:PHE381 4.3 18.7 1.0 N B:ARG378 4.5 19.9 1.0 N B:LEU373 4.6 20.0 1.0 O B:HOH876 4.6 31.2 1.0 CA B:PHE381 4.7 15.9 1.0 CG2 B:THR380 4.8 23.9 1.0 CA B:ARG378 4.8 21.5 1.0 CA B:LEU373 4.8 19.5 1.0 N B:ARG472 4.9 16.8 1.0 CB B:ASP375 4.9 23.5 1.0 N B:ASP375 4.9 20.5 1.0 C B:ARG378 4.9 21.1 1.0 C B:LEU373 5.0 20.9 1.0 N B:GLY376 5.0 26.8 1.0

H.Sakurama, S.Fushinobu, M.Hidaka, E.Yoshida, Y.Honda, H.Ashida, M.Kitaoka, H.Kumagai, K.Yamamoto, T.Katayama. 1,3-1,4-Alpha-L-Fucosynthase That Specifically Introduces Lewis A/X Antigens Into Type-1/2 Chains J.Biol.Chem. V. 287 16709 2012.
ISSN: ISSN 0021-9258
PubMed: 22451675
DOI: 10.1074/JBC.M111.333781