Sodium in PDB 4wxs: Crystal Structure of the E396D Snp Variant of the Myocilin Olfactomedin Domain

The structure of Crystal Structure of the E396D Snp Variant of the Myocilin Olfactomedin Domain, PDB code: 4wxs was solved by R.K.Donegan, D.M.Freeman, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.880, 86.650, 87.440, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The structure of Crystal Structure of the E396D Snp Variant of the Myocilin Olfactomedin Domain also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the E396D Snp Variant of the Myocilin Olfactomedin Domain (pdb code 4wxs). 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 E396D Snp Variant of the Myocilin Olfactomedin Domain, PDB code: 4wxs:

Sodium binding site 1 out of 1 in the Crystal Structure of the E396D Snp Variant of the Myocilin Olfactomedin Domain


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 E396D Snp Variant of the Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:17.9 occ:1.00 O A:LEU381 2.4 12.4 1.0 OD1 A:ASP380 2.4 12.8 1.0 O A:HOH832 2.4 14.1 1.0 OD2 A:ASP478 2.4 15.6 1.0 O A:GLY326 2.6 13.5 1.0 OD1 A:ASP478 2.7 17.0 1.0 CG A:ASP478 2.9 17.6 1.0 C A:GLY326 3.2 11.6 1.0 C A:LEU381 3.4 11.5 1.0 O A:HOH833 3.5 12.9 1.0 CG A:ASP380 3.6 10.3 1.0 CA A:GLY326 3.6 9.0 1.0 N A:LEU381 3.7 9.6 1.0 CG1 A:VAL328 3.7 10.5 1.0 O A:HOH836 3.8 11.6 1.0 O A:ALA327 3.8 9.4 1.0 CA A:CA601 3.9 12.6 1.0 CA A:LEU381 4.0 13.1 1.0 C A:ASP380 4.2 11.0 1.0 N A:ALA327 4.2 10.9 1.0 O A:HOH898 4.3 13.9 1.0 OD2 A:ASP380 4.3 12.6 1.0 C A:ALA327 4.4 12.2 1.0 CB A:ASP478 4.4 6.6 1.0 O A:THR325 4.5 18.8 1.0 CA A:ASP380 4.5 10.2 1.0 CB A:LEU381 4.5 10.9 1.0 N A:ALA382 4.5 9.6 1.0 CB A:ASP380 4.6 9.3 1.0 CA A:ALA382 4.8 11.1 1.0 CA A:ALA327 4.8 9.8 1.0 N A:GLY326 4.8 11.6 1.0 O A:ASP380 4.9 13.3 1.0 O A:HOH843 5.0 14.2 1.0

R.K.Donegan, S.E.Hill, D.M.Freeman, E.Nguyen, S.D.Orwig, K.C.Turnage, R.L.Lieberman. Structural Basis For Misfolding in Myocilin-Associated Glaucoma. Hum.Mol.Genet. V. 24 2111 2015.
ISSN: ESSN 1460-2083
PubMed: 25524706
DOI: 10.1093/HMG/DDU730