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Sodium in PDB 4q56: Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac)

Protein crystallography data

The structure of Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac), PDB code: 4q56 was solved by A.J.Pietrzyk, A.Bujacz, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.92 / 1.38
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 47.900, 47.900, 281.530, 90.00, 90.00, 120.00
R / Rfree (%) 13.7 / 16.8

Other elements in 4q56:

The structure of Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac) (pdb code 4q56). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac), PDB code: 4q56:

Sodium binding site 1 out of 1 in 4q56

Go back to Sodium Binding Sites List in 4q56
Sodium binding site 1 out of 1 in the Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Helix Aspersa Agglutinin with Natural Glycosylation and N-Acetyl-Alpha-D-Galactosamine (Galnac) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:18.8
occ:0.33
O A:HOH337 2.5 18.6 0.3
O A:GLN59 2.5 18.2 1.0
OE1 A:GLN59 2.5 24.5 1.0
O A:HOH396 2.7 40.5 0.3
C A:GLN59 3.4 15.9 1.0
CD A:GLN59 3.6 24.0 1.0
CB A:GLN59 3.6 19.0 1.0
CA A:GLN59 3.9 15.9 1.0
CG A:GLN59 4.2 21.8 1.0
N A:SER60 4.4 16.9 1.0
O A:HOH369 4.7 40.0 1.0
NE2 A:GLN59 4.7 34.5 1.0
O A:HOH336 4.7 18.0 1.0
CA A:SER60 4.7 18.1 1.0

Reference:

A.J.Pietrzyk, A.Bujacz, P.Mak, B.Potempa, T.Niedziela. Structural Studies of Helix Aspersa Agglutinin Complexed with Galnac: A Lectin That Serves As A Diagnostic Tool. Int.J.Biol.Macromol. V. 81 1059 2015.
ISSN: ISSN 0141-8130
PubMed: 26416237
DOI: 10.1016/J.IJBIOMAC.2015.09.044
Page generated: Tue Dec 15 07:05:00 2020

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