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Sodium in PDB 3uet: Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II

Enzymatic activity of Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II

All present enzymatic activity of Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II:
3.2.1.111;

Protein crystallography data

The structure of Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II, PDB code: 3uet 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) 32.05 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.588, 105.971, 120.715, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II (pdb code 3uet). 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 D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II, PDB code: 3uet:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3uet

Go back to Sodium Binding Sites List in 3uet
Sodium binding site 1 out of 2 in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II


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 D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:26.4
occ:1.00
 O A:ASN377 2.2 21.3 1.0
O A:HIS372 2.4 28.9 1.0
OG1 A:THR380 2.4 26.2 1.0
O A:THR380 2.6 25.1 1.0
OD1 A:ASP375 2.6 22.4 1.0
O A:SER471 2.8 28.6 1.0
C A:ASN377 3.4 25.6 1.0
C A:THR380 3.4 24.4 1.0
CG A:ASP375 3.5 25.6 1.0
C A:HIS372 3.5 26.8 1.0
CB A:THR380 3.6 25.6 1.0
OD2 A:ASP375 3.7 27.6 1.0
C A:SER471 3.8 25.8 1.0
CA A:THR380 3.8 25.6 1.0
N A:THR380 3.8 25.5 1.0
N A:ASN377 3.9 24.2 1.0
CA A:ASN377 4.0 25.7 1.0
CA A:HIS372 4.1 25.0 1.0
CA A:SER471 4.2 24.4 1.0
CB A:ASN377 4.2 26.1 1.0
CB A:HIS372 4.3 26.0 1.0
N A:ARG378 4.4 26.8 1.0
N A:PHE381 4.4 26.5 1.0
CB A:SER471 4.4 22.8 1.0
O A:HOH540 4.6 29.1 1.0
CA A:ARG378 4.6 26.2 1.0
N A:LEU373 4.7 24.8 1.0
C A:ARG378 4.8 29.4 1.0
CA A:PHE381 4.8 22.9 1.0
CG2 A:THR380 4.9 28.1 1.0
N A:ASP375 4.9 29.2 1.0
N A:ASP379 4.9 29.9 1.0
CB A:ASP375 4.9 23.7 1.0
N A:ARG472 5.0 30.0 1.0

Sodium binding site 2 out of 2 in 3uet

Go back to Sodium Binding Sites List in 3uet
Sodium binding site 2 out of 2 in the Crystal Structure of Alpha-1,3/4-Fucosidase From Bifidobacterium Longum Subsp. Infantis D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II


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 D172A/E217A Mutant Complexed with Lacto-N- Fucopentaose II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:26.6
occ:1.00
 O B:HIS372 2.2 27.8 1.0
O B:ASN377 2.3 26.2 1.0
O B:THR380 2.4 23.9 1.0
OG1 B:THR380 2.6 23.1 1.0
O B:SER471 2.7 26.6 1.0
OD1 B:ASP375 2.8 30.4 1.0
C B:THR380 3.3 24.1 1.0
C B:HIS372 3.3 26.5 1.0
C B:ASN377 3.5 26.2 1.0
C B:SER471 3.6 29.2 1.0
CG B:ASP375 3.6 29.7 1.0
OD2 B:ASP375 3.8 25.9 1.0
CB B:THR380 3.8 23.0 1.0
CA B:THR380 3.8 25.9 1.0
N B:THR380 3.8 23.4 1.0
CA B:SER471 3.9 26.4 1.0
CA B:HIS372 3.9 25.0 1.0
N B:ASN377 4.0 24.0 1.0
CB B:HIS372 4.1 26.2 1.0
CB B:SER471 4.1 27.6 1.0
CA B:ASN377 4.1 26.0 1.0
N B:PHE381 4.2 24.4 1.0
CB B:ASN377 4.2 24.1 1.0
N B:LEU373 4.5 29.0 1.0
N B:ARG378 4.6 26.0 1.0
CA B:PHE381 4.6 25.5 1.0
O B:HOH708 4.7 38.0 1.0
N B:ARG472 4.8 26.2 1.0
CA B:ARG378 4.8 29.5 1.0
CA B:LEU373 4.8 28.4 1.0
N B:GLY376 4.9 24.3 1.0
C B:ARG378 4.9 29.0 1.0
CG2 B:THR380 5.0 20.9 1.0
C B:LEU373 5.0 28.8 1.0

Reference:

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
Page generated: Tue Dec 15 06:27:15 2020

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