Sodium in PDB 5gzf: Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain

The structure of Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain, PDB code: 5gzf was solved by J.Y.Su, Y.L.Si, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.41 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.871, 48.871, 159.725, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.8

The structure of Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Sodium atom in the Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain (pdb code 5gzf). 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 Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain, PDB code: 5gzf:

Sodium binding site 1 out of 1 in the Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:35.0 occ:1.00 O3 A:LAT201 3.1 37.1 1.0 NH2 A:ARG59 3.1 38.0 1.0 NE2 A:GLN47 3.2 28.5 1.0 NH1 A:ARG59 3.4 37.0 1.0 CZ A:ARG59 3.7 38.5 1.0 CZ2 A:TRP86 3.8 34.0 1.0 O A:HOH341 3.8 40.3 1.0 OE1 A:GLN47 3.8 36.3 1.0 NH2 A:ARG45 3.9 34.9 1.0 CD A:GLN47 3.9 32.7 1.0 C3 A:LAT201 4.0 37.5 1.0 CE1 A:HIS65 4.3 32.4 1.0 C4 A:LAT201 4.3 34.6 1.0 O4 A:LAT201 4.6 35.6 1.0 CH2 A:TRP86 4.6 33.6 1.0 CE2 A:TRP86 4.6 34.9 1.0 NE1 A:TRP86 4.8 37.7 1.0 NE2 A:HIS65 4.8 34.1 1.0 ND1 A:HIS65 5.0 28.5 1.0 NE A:ARG59 5.0 37.0 1.0

Y.L.Si, Y.Wang, J.Gao, C.Song, S.Feng, Y.Zhou, G.Tai, J.Y.Su. Crystallization of Galectin-8 Linker Reveals Intricate Relationship Between the N-Terminal Tail and the Linker Int J Mol Sci V. 17 2088 2016.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS17122088