Sodium in PDB 8frr: Wild-Type Myocilin Olfactomedin Domain

The structure of Wild-Type Myocilin Olfactomedin Domain, PDB code: 8frr was solved by M.T.Ma, R.L.Lieberman, D.J.E.Huard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.91 / 1.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.468, 50.527, 50.873, 90, 96.25, 90
R / Rfree (%)	14 / 15.5

The structure of Wild-Type Myocilin Olfactomedin Domain also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Wild-Type Myocilin Olfactomedin Domain (pdb code 8frr). 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 Wild-Type Myocilin Olfactomedin Domain, PDB code: 8frr:

Sodium binding site 1 out of 1 in the Wild-Type 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 Wild-Type Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:9.7 occ:1.00 O A:LEU381 2.3 9.0 1.0 OD1 A:ASP380 2.3 9.8 1.0 O A:HOH744 2.4 10.1 1.0 OD2 A:ASP478 2.4 12.0 1.0 O A:GLY326 2.5 9.7 1.0 OD1 A:ASP478 2.8 10.2 1.0 CG A:ASP478 3.0 9.7 1.0 HA2 A:GLY326 3.1 11.2 1.0 C A:GLY326 3.3 9.0 1.0 HG13 A:VAL328 3.3 12.9 1.0 H A:LEU381 3.3 10.1 1.0 C A:LEU381 3.4 8.3 1.0 HG12 A:VAL328 3.5 12.9 1.0 CG A:ASP380 3.6 9.6 1.0 N A:LEU381 3.6 8.4 1.0 O A:HOH821 3.6 11.1 1.0 CA A:GLY326 3.7 9.4 1.0 O A:HOH802 3.8 8.6 1.0 CG1 A:VAL328 3.8 10.8 1.0 O A:ALA327 3.8 9.1 1.0 CA A:CA602 4.0 7.6 1.0 HA A:ASP380 4.0 10.1 1.0 HB2 A:LEU381 4.0 12.5 1.0 CA A:LEU381 4.0 9.4 1.0 HG11 A:VAL328 4.0 12.9 1.0 HA3 A:GLY326 4.1 11.2 1.0 C A:ASP380 4.1 9.2 1.0 HA A:ALA382 4.2 10.8 1.0 N A:ALA327 4.3 9.0 1.0 O A:HOH730 4.3 11.9 1.0 OD2 A:ASP380 4.3 9.4 1.0 C A:ALA327 4.3 8.6 1.0 CA A:ASP380 4.4 8.4 1.0 N A:ALA382 4.5 9.5 1.0 CB A:ASP478 4.5 8.9 1.0 CB A:LEU381 4.5 10.5 1.0 CB A:ASP380 4.6 8.8 1.0 O A:THR325 4.6 9.5 1.0 CA A:ALA382 4.8 9.0 1.0 CA A:ALA327 4.8 9.0 1.0 HB3 A:ASP478 4.8 10.6 1.0 O A:HOH896 4.9 11.1 1.0 HB2 A:ASP478 4.9 10.6 1.0 HA A:LEU381 4.9 11.3 1.0 N A:GLY326 4.9 9.1 1.0 HB2 A:ALA382 4.9 13.2 1.0 H A:ALA327 4.9 10.8 1.0 O A:ASP380 4.9 10.9 1.0 HA A:ALA327 5.0 10.8 1.0 HB3 A:LEU381 5.0 12.5 1.0

E.G.Saccuzzo, M.D.Mebrat, H.F.Scelsi, M.Kim, M.T.Ma, X.Su, S.E.Hill, E.Rheaume, R.Li, M.P.Torres, J.C.Gumbart, W.D.Van Horn, R.L.Lieberman. Competition Between Inside-Out Unfolding and Pathogenic Aggregation in An Amyloid-Forming Beta-Propeller. Nat Commun V. 15 155 2024.
ISSN: ESSN 2041-1723
PubMed: 38168102
DOI: 10.1038/S41467-023-44479-2