Sodium in PDB 5t7u: Crystal Structure of Galectin-8N in Complex with Glycerol

The structure of Crystal Structure of Galectin-8N in Complex with Glycerol, PDB code: 5t7u was solved by M.H.Bohari, X.Yu, H.Blanchard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.73 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.400, 50.300, 69.390, 90.00, 90.00, 90.00
R / Rfree (%)	11.8 / 14.7

The structure of Crystal Structure of Galectin-8N in Complex with Glycerol also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Galectin-8N in Complex with Glycerol (pdb code 5t7u). 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 Crystal Structure of Galectin-8N in Complex with Glycerol, PDB code: 5t7u:

Sodium binding site 1 out of 1 in the Crystal Structure of Galectin-8N in Complex with Glycerol


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 Galectin-8N in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:29.2 occ:1.00 O A:HOH486 2.5 39.6 1.0 O A:HOH316 2.9 10.9 1.0 O A:HOH494 3.0 28.5 1.0 NH2 A:ARG59 3.5 14.8 1.0 CZ A:TYR141 3.7 9.7 1.0 CZ A:ARG59 3.8 14.0 1.0 NE A:ARG59 3.8 13.4 1.0 CE1 A:TYR141 3.8 10.2 1.0 CE2 A:TYR141 3.9 9.5 1.0 OH A:TYR141 4.0 10.3 1.0 CD1 A:TYR141 4.3 10.1 1.0 CD2 A:TYR141 4.3 9.3 1.0 O A:HOH417 4.4 11.6 1.0 CG A:TYR141 4.5 9.2 1.0 O A:HOH405 4.5 13.1 1.0 NH1 A:ARG59 4.6 15.4 1.0 OD2 A:ASP49 4.7 8.9 1.0 CD A:ARG59 4.8 13.9 1.0 NE2 A:GLN47 4.8 9.6 1.0 CL A:CL204 4.9 24.7 1.0 OE1 A:GLN51 5.0 9.7 1.0

M.H.Bohari, X.Yu, Y.Zick, H.Blanchard. Structure-Based Rationale For Differential Recognition of Lacto- and Neolacto- Series Glycosphingolipids By the N-Terminal Domain of Human Galectin-8. Sci Rep V. 6 39556 2016.
ISSN: ESSN 2045-2322
PubMed: 28000747
DOI: 10.1038/SREP39556