Sodium in PDB 6ou1: Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain

The structure of Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain, PDB code: 6ou1 was solved by S.E.Hill, M.S.Kwon, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.71 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.357, 66.889, 80.999, 90.00, 95.19, 90.00
R / Rfree (%)	16.8 / 19.5

The structure of Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain (pdb code 6ou1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain, PDB code: 6ou1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Computationally-Derived 21-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 Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:16.1 occ:1.00 O A:LEU381 2.2 19.2 1.0 OD1 A:ASP380 2.3 18.2 1.0 OD2 A:ASP478 2.4 21.9 1.0 O A:HOH724 2.5 17.8 1.0 O A:GLY326 2.6 17.1 1.0 OD1 A:ASP478 2.8 23.7 1.0 CG A:ASP478 3.0 19.7 1.0 HA2 A:GLY326 3.0 20.3 1.0 C A:GLY326 3.2 17.2 1.0 HG13 A:VAL328 3.2 21.7 1.0 H A:LEU381 3.3 20.9 1.0 C A:LEU381 3.3 18.6 1.0 HG12 A:VAL328 3.3 21.7 1.0 N A:LEU381 3.5 17.4 1.0 CG A:ASP380 3.5 17.2 1.0 CA A:GLY326 3.6 16.9 1.0 O A:HOH760 3.6 18.0 1.0 CG1 A:VAL328 3.7 18.0 1.0 O A:HOH744 3.7 17.4 1.0 O A:ALA327 3.8 19.2 1.0 HG11 A:VAL328 3.9 21.7 1.0 HA A:ASP380 3.9 16.3 1.0 HB2 A:LEU381 3.9 22.6 1.0 CA A:LEU381 3.9 18.1 1.0 HA3 A:GLY326 4.0 20.3 1.0 CA A:CA601 4.0 7.6 1.0 C A:ASP380 4.1 16.4 1.0 HA A:ALA382 4.2 19.4 1.0 N A:ALA327 4.2 15.7 1.0 O A:HOH732 4.2 20.5 1.0 C A:ALA327 4.3 16.1 1.0 OD2 A:ASP380 4.3 10.2 1.0 CA A:ASP380 4.4 13.5 1.0 N A:ALA382 4.5 16.1 1.0 CB A:LEU381 4.5 18.8 1.0 CB A:ASP478 4.5 16.8 1.0 O A:THR325 4.5 19.2 1.0 CB A:ASP380 4.6 15.1 1.0 CA A:ALA327 4.8 15.1 1.0 CA A:ALA382 4.8 16.1 1.0 HB3 A:ASP478 4.8 20.2 1.0 HB2 A:ALA382 4.8 20.4 1.0 HB2 A:ASP478 4.8 20.2 1.0 HA A:LEU381 4.8 21.8 1.0 H A:ALA327 4.8 18.9 1.0 O A:ASP380 4.9 17.9 1.0 N A:GLY326 4.9 16.7 1.0 HA A:ALA327 4.9 18.2 1.0 O A:HOH794 4.9 20.3 1.0 HG2 A:MET476 5.0 23.3 1.0 HB3 A:LEU381 5.0 22.6 1.0 N A:VAL328 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Computationally-Derived 21-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 2 of Crystal Structure of the Computationally-Derived 21-Variant of the Myocilin Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:34.4 occ:1.00 O B:HOH701 2.1 21.8 1.0 OD2 B:ASP478 2.4 36.2 1.0 HA2 B:GLY326 2.6 30.2 1.0 OD1 B:ASP380 2.9 24.6 1.0 OD1 B:ASP478 3.0 29.7 1.0 O B:LEU381 3.0 17.9 1.0 O B:GLY326 3.0 26.5 1.0 CG B:ASP478 3.0 35.3 1.0 C B:GLY326 3.1 28.5 1.0 CA B:GLY326 3.2 25.1 1.0 HA3 B:GLY326 3.3 30.2 1.0 HG13 B:VAL328 3.6 25.2 1.0 H B:LEU381 3.6 22.9 1.0 HG12 B:VAL328 3.7 25.2 1.0 CA B:CA601 3.8 49.7 1.0 N B:ALA327 3.8 25.3 1.0 O B:ALA327 3.8 26.6 1.0 C B:LEU381 4.0 19.6 1.0 HB2 B:LEU381 4.0 25.4 1.0 N B:LEU381 4.1 19.0 1.0 CG1 B:VAL328 4.1 21.0 1.0 CG B:ASP380 4.1 26.7 1.0 HG2 B:MET476 4.2 40.7 1.0 H B:ALA327 4.2 30.4 1.0 O B:HOH714 4.3 30.0 1.0 HG11 B:VAL328 4.3 25.2 1.0 C B:ALA327 4.3 25.7 1.0 HA B:ASP380 4.4 23.5 1.0 O B:HOH772 4.4 28.9 1.0 CA B:LEU381 4.5 20.2 1.0 N B:GLY326 4.5 25.9 1.0 CB B:ASP478 4.5 30.6 1.0 CA B:ALA327 4.6 26.4 1.0 O B:THR325 4.6 34.8 1.0 HA B:ALA327 4.7 31.7 1.0 CB B:LEU381 4.7 21.1 1.0 C B:ASP380 4.8 21.6 1.0 OD2 B:ASP380 4.8 24.5 1.0 HB2 B:ASP478 4.8 36.7 1.0 HA B:ALA382 4.8 25.2 1.0 CA B:ASP380 5.0 19.6 1.0 HB3 B:ASP478 5.0 36.7 1.0 CG B:MET476 5.0 33.9 1.0

S.E.Hill, M.S.Kwon, M.D.Martin, A.Suntharalingam, A.Hazel, C.A.Dickey, J.C.Gumbart, R.L.Lieberman. Calcium-Depleted Variants of the Myocilin Olfactomedin Domain Reveal A Stable Alternative Conformation with An Unwound Helix To Be Published.