Sodium in PDB 7sib: Myocilin Olf Mutant K500R

The structure of Myocilin Olf Mutant K500R, PDB code: 7sib was solved by H.S.Scelsi, B.M.Barlow, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.75 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.301, 50.776, 50.651, 90, 96.31, 90
R / Rfree (%)	14.7 / 18.2

The structure of Myocilin Olf Mutant K500R also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Myocilin Olf Mutant K500R (pdb code 7sib). 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 Myocilin Olf Mutant K500R, PDB code: 7sib:

Sodium binding site 1 out of 1 in the Myocilin Olf Mutant K500R


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Myocilin Olf Mutant K500R within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:4.6 occ:1.00 O A:LEU381 2.3 4.8 1.0 OD1 A:ASP380 2.3 5.2 1.0 OD2 A:ASP478 2.4 6.3 1.0 O A:HOH764 2.4 4.8 1.0 O A:GLY326 2.6 4.2 1.0 OD1 A:ASP478 2.8 7.6 1.0 CG A:ASP478 3.0 5.7 1.0 C A:GLY326 3.3 5.4 1.0 C A:LEU381 3.3 3.6 1.0 CG A:ASP380 3.5 6.2 1.0 N A:LEU381 3.6 4.4 1.0 O A:HOH852 3.6 4.5 1.0 CA A:GLY326 3.7 2.5 1.0 O A:HOH809 3.7 3.7 1.0 CG1 A:VAL328 3.8 3.4 1.0 O A:ALA327 3.8 5.9 1.0 CA A:CA602 3.9 4.3 1.0 CA A:LEU381 4.0 4.0 1.0 C A:ASP380 4.1 4.5 1.0 O A:HOH723 4.2 6.3 1.0 OD2 A:ASP380 4.3 4.6 1.0 N A:ALA327 4.3 3.7 1.0 C A:ALA327 4.4 4.6 1.0 CA A:ASP380 4.4 3.3 1.0 N A:ALA382 4.5 2.9 1.0 CB A:ASP478 4.5 4.6 1.0 CB A:LEU381 4.5 5.1 1.0 CB A:ASP380 4.6 1.8 1.0 O A:THR325 4.6 1.9 1.0 CA A:ALA382 4.8 2.6 1.0 CA A:ALA327 4.8 4.5 1.0 O A:HOH879 4.9 6.0 1.0 O A:ASP380 4.9 6.5 1.0 N A:GLY326 4.9 3.1 1.0

H.F.Scelsi, K.R.Hill, B.M.Barlow, M.D.Martin, R.L.Lieberman. Disambiguation of Benign and Misfolded Glaucoma-Causing Myocilin Variants on the Basis of Protein Thermal Stability. Dis Model Mech 2022.
ISSN: ISSN 1754-8411
PubMed: 36579626
DOI: 10.1242/DMM.049816