Sodium in PDB 6nax: Olfactomedin Domain of Mouse Myocilin

The structure of Olfactomedin Domain of Mouse Myocilin, PDB code: 6nax was solved by A.C.Patterson-Orazem, S.E.Hill, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.10 / 1.55
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	111.955, 111.955, 44.129, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.8

The structure of Olfactomedin Domain of Mouse Myocilin also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Olfactomedin Domain of Mouse Myocilin (pdb code 6nax). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Olfactomedin Domain of Mouse Myocilin, PDB code: 6nax:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Olfactomedin Domain of Mouse Myocilin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Olfactomedin Domain of Mouse Myocilin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:7.0 occ:1.00 O A:LEU367 2.3 6.9 1.0 OD1 A:ASP366 2.3 6.9 1.0 O A:HOH640 2.4 6.6 1.0 OD2 A:ASP464 2.4 7.8 1.0 O A:GLY312 2.5 6.9 1.0 OD1 A:ASP464 2.8 6.6 1.0 CG A:ASP464 2.9 6.7 1.0 C A:GLY312 3.2 5.9 1.0 C A:LEU367 3.3 6.0 1.0 N A:LEU367 3.5 5.6 1.0 CG A:ASP366 3.6 6.0 1.0 O A:HOH732 3.6 7.5 1.0 CA A:GLY312 3.6 7.0 1.0 O A:HOH739 3.8 7.0 1.0 CG1 A:VAL314 3.8 8.3 1.0 O A:ALA313 3.8 7.5 1.0 CA A:LEU367 3.9 6.5 1.0 CA A:CA501 3.9 6.1 1.0 C A:ASP366 4.1 5.4 1.0 N A:ALA313 4.3 5.8 1.0 O A:HOH619 4.3 7.9 1.0 C A:ALA313 4.3 5.4 1.0 OD2 A:ASP366 4.3 7.7 1.0 CA A:ASP366 4.4 5.7 1.0 CB A:ASP464 4.5 6.3 1.0 N A:ALA368 4.5 6.2 1.0 CB A:LEU367 4.5 7.0 1.0 CB A:ASP366 4.6 5.9 1.0 O A:THR311 4.6 7.8 1.0 CA A:ALA313 4.8 6.4 1.0 CA A:ALA368 4.8 4.5 1.0 O A:HOH789 4.8 7.8 1.0 O A:ASP366 4.9 7.7 1.0 N A:GLY312 4.9 8.1 1.0

Sodium binding site 2 out of 2 in the Olfactomedin Domain of Mouse Myocilin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Olfactomedin Domain of Mouse Myocilin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:6.5 occ:1.00 O B:LEU367 2.3 7.4 1.0 OD1 B:ASP366 2.3 7.3 1.0 O B:HOH648 2.4 6.7 1.0 OD2 B:ASP464 2.4 8.2 1.0 O B:GLY312 2.5 6.8 1.0 OD1 B:ASP464 2.8 7.1 1.0 CG B:ASP464 2.9 6.8 1.0 C B:GLY312 3.2 6.0 1.0 C B:LEU367 3.4 6.2 1.0 N B:LEU367 3.5 5.8 1.0 CG B:ASP366 3.6 6.4 1.0 O B:HOH721 3.6 8.0 1.0 CA B:GLY312 3.6 7.3 1.0 O B:HOH725 3.8 6.7 1.0 CG1 B:VAL314 3.8 8.5 1.0 O B:ALA313 3.8 8.1 1.0 CA B:CA501 3.9 6.0 1.0 CA B:LEU367 3.9 6.3 1.0 C B:ASP366 4.1 6.1 1.0 N B:ALA313 4.3 5.8 1.0 O B:HOH610 4.3 7.7 1.0 C B:ALA313 4.3 6.3 1.0 OD2 B:ASP366 4.3 7.6 1.0 CA B:ASP366 4.4 5.5 1.0 CB B:ASP464 4.4 5.9 1.0 CB B:LEU367 4.5 7.5 1.0 N B:ALA368 4.5 6.1 1.0 CB B:ASP366 4.6 5.1 1.0 O B:THR311 4.6 7.2 1.0 CA B:ALA313 4.8 6.8 1.0 O B:HOH781 4.8 8.7 1.0 CA B:ALA368 4.8 5.3 1.0 O B:ASP366 4.9 7.2 1.0 N B:GLY312 4.9 8.2 1.0

A.C.Patterson-Orazem, S.E.Hill, Y.Wang, I.M.Dominic, C.K.Hall, R.L.Lieberman. Differential Misfolding Properties of Glaucoma-Associated Olfactomedin Domains From Humans and Mice. Biochemistry V. 58 1718 2019.
ISSN: ISSN 1520-4995
PubMed: 30802039
DOI: 10.1021/ACS.BIOCHEM.8B01309