Sodium in PDB 4xat: Crystal Structure of the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1

The structure of Crystal Structure of the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1, PDB code: 4xat was solved by S.E.Hill, E.Nguyen, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.27 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.681, 68.016, 95.659, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.4

The structure of Crystal Structure of the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1 (pdb code 4xat). 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 the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1, PDB code: 4xat:

Sodium binding site 1 out of 1 in the Crystal Structure of the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1


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 the Olfactomedin Domain From Noelin/Pancortin/Olfactomedin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:20.6 occ:1.00 O A:LEU357 2.2 18.2 1.0 OD2 A:ASP453 2.3 18.2 1.0 OD1 A:ASP356 2.3 19.6 1.0 O A:HOH646 2.4 20.4 1.0 O A:GLY302 2.9 21.2 1.0 O A:GLN303 3.0 19.1 1.0 C A:GLY302 3.1 18.6 1.0 C A:LEU357 3.3 19.1 1.0 CG A:ASP453 3.3 18.3 1.0 CA A:GLY302 3.5 18.7 1.0 N A:LEU357 3.5 18.0 1.0 CG A:ASP356 3.6 21.7 1.0 OD1 A:ASP453 3.6 17.3 1.0 O A:HOH666 3.7 16.9 1.0 O A:HOH667 3.8 19.7 1.0 C A:GLN303 3.8 19.3 1.0 N A:GLN303 3.9 17.1 1.0 CA A:LEU357 4.0 17.8 1.0 C A:ASP356 4.2 17.4 1.0 N A:MET358 4.3 16.9 1.0 OD2 A:ASP356 4.3 19.1 1.0 CA A:GLN303 4.4 16.3 1.0 CB A:MET358 4.4 15.9 1.0 CA A:MET358 4.4 16.7 1.0 CA A:ASP356 4.5 20.8 1.0 CA A:CA501 4.5 18.4 1.0 CB A:ASP453 4.6 17.7 1.0 CB A:VAL304 4.6 15.4 1.0 O A:THR301 4.6 18.4 1.0 N A:VAL304 4.6 20.1 1.0 CB A:ASP356 4.6 16.1 1.0 CB A:LEU357 4.7 18.8 1.0 N A:GLY302 4.7 20.9 1.0 CE A:MET358 4.8 16.4 1.0 CA A:VAL304 4.9 17.9 1.0

S.E.Hill, R.K.Donegan, E.Nguyen, T.M.Desai, R.L.Lieberman. Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies. Plos One V. 10 30888 2015.
ISSN: ESSN 1932-6203
PubMed: 26121352
DOI: 10.1371/JOURNAL.PONE.0130888