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

Protein crystallography data

The structure of Galectin-8 N-Terminal Domain Carbohydrate Recognition Domain, PDB code: 5gzg 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) 19.47 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 49.127, 49.127, 159.666, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.8

Other elements in 5gzg:

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

Nickel (Ni) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 5gzg

Go back to Sodium Binding Sites List in 5gzg
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:39.7
occ:1.00
NH2 A:ARG59 3.0 42.5 1.0
O3 A:LAT201 3.2 37.7 1.0
NE2 A:GLN47 3.3 33.3 1.0
NH1 A:ARG59 3.4 44.2 1.0
CZ A:ARG59 3.6 42.3 1.0
CZ2 A:TRP86 3.8 37.3 1.0
O A:HOH317 3.8 42.5 1.0
OE1 A:GLN47 3.8 42.8 1.0
NH2 A:ARG45 3.9 40.8 1.0
CD A:GLN47 4.0 39.7 1.0
C3 A:LAT201 4.0 43.1 1.0
C4 A:LAT201 4.3 38.7 1.0
CE1 A:HIS65 4.3 37.6 1.0
O4 A:LAT201 4.6 38.1 1.0
CE2 A:TRP86 4.6 37.6 1.0
CH2 A:TRP86 4.7 36.4 1.0
NE1 A:TRP86 4.7 38.0 1.0
NE2 A:HIS65 4.9 34.7 1.0
NE A:ARG59 4.9 38.7 1.0
ND1 A:HIS65 5.0 33.5 1.0

Reference:

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
Page generated: Tue Dec 15 11:02:10 2020

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