Sodium in PDB 6pkd: Myocilin Olf Mutant N428D/D478H

The structure of Myocilin Olf Mutant N428D/D478H, PDB code: 6pkd was solved by R.L.Lieberman, S.E.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.63 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.547, 47.342, 97.076, 90.00, 100.20, 90.00
R / Rfree (%)	18.2 / 20.8

The binding sites of Sodium atom in the Myocilin Olf Mutant N428D/D478H (pdb code 6pkd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Myocilin Olf Mutant N428D/D478H, PDB code: 6pkd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Myocilin Olf Mutant N428D/D478H


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 N428D/D478H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:57.6 occ:1.00 O A:HOH719 2.1 29.0 1.0 O A:HOH830 2.2 31.8 1.0 O A:HOH707 2.2 28.3 1.0 O A:HOH702 2.2 40.1 1.0 OD2 A:ASP380 2.2 32.9 1.0 OD1 A:ASP428 2.5 19.7 1.0 CG A:ASP380 2.9 41.9 1.0 OD1 A:ASP380 2.9 44.0 1.0 CG A:ASP428 3.4 20.1 1.0 OD2 A:ASP428 3.5 19.8 1.0 HE2 A:TYR371 3.7 25.4 1.0 H A:ILE477 4.0 22.6 1.0 O A:HOH845 4.0 33.4 1.0 H A:ALA429 4.0 17.9 1.0 HH A:TYR371 4.1 26.0 1.0 O A:HOH703 4.2 33.5 1.0 CB A:ASP380 4.3 25.6 1.0 O A:ILE477 4.3 20.5 1.0 O A:ALA429 4.3 17.0 1.0 O A:HOH826 4.3 24.6 1.0 HB2 A:MET476 4.3 30.0 1.0 HB2 A:ASP380 4.4 30.9 1.0 CE2 A:TYR371 4.4 21.0 1.0 HG22 A:ILE477 4.4 22.9 1.0 HA A:MET476 4.5 25.5 1.0 O A:HOH741 4.5 34.1 1.0 O A:THR325 4.6 43.8 1.0 HB3 A:ASP380 4.7 30.9 1.0 HA A:ASP428 4.7 18.3 1.0 HB3 A:MET476 4.8 30.0 1.0 CB A:ASP428 4.8 16.4 1.0 OH A:TYR371 4.8 21.5 1.0 N A:ILE477 4.8 18.7 1.0 N A:ALA429 4.9 14.8 1.0 CB A:MET476 4.9 24.8 1.0

Sodium binding site 2 out of 2 in the Myocilin Olf Mutant N428D/D478H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Myocilin Olf Mutant N428D/D478H within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:31.7 occ:1.00 OD2 B:ASP380 2.1 29.3 1.0 O B:HOH742 2.1 25.8 1.0 O B:HOH708 2.3 30.2 1.0 OD1 B:ASP428 2.3 17.6 1.0 O B:HOH776 2.3 32.3 1.0 CG B:ASP380 2.8 33.8 1.0 OD1 B:ASP380 2.8 35.9 1.0 CG B:ASP428 3.1 18.8 1.0 OD2 B:ASP428 3.3 19.0 1.0 H B:ILE477 3.7 20.6 1.0 O B:ILE477 3.7 19.4 1.0 H B:ALA429 3.8 16.5 1.0 O B:ALA429 3.9 16.1 1.0 HG23 B:ILE477 3.9 19.3 1.0 O B:HOH795 3.9 28.0 1.0 HE2 B:TYR371 4.0 22.6 1.0 HH B:TYR371 4.2 22.0 1.0 CB B:ASP380 4.3 24.4 1.0 O B:HOH849 4.4 31.4 1.0 HB2 B:MET476 4.5 26.8 1.0 HB3 B:ASP380 4.6 29.5 1.0 HB2 B:ASP380 4.6 29.5 1.0 O B:HOH710 4.6 33.6 1.0 CE1 B:HIS478 4.6 34.6 1.0 HA B:MET476 4.6 22.7 1.0 N B:ILE477 4.6 16.9 1.0 CB B:ASP428 4.6 17.0 1.0 N B:ALA429 4.6 13.6 1.0 CE2 B:TYR371 4.6 18.6 1.0 HA B:ASP428 4.6 18.3 1.0 CG2 B:ILE477 4.8 15.9 1.0 C B:ILE477 4.8 20.3 1.0 OH B:TYR371 4.9 18.2 1.0 HG21 B:ILE477 5.0 19.3 1.0 NE2 B:HIS478 5.0 34.0 1.0 C B:ALA429 5.0 17.7 1.0

S.E.Hill, H.Cho, P.Raut, R.L.Lieberman. Calcium-Ligand Variants of the Myocilin Olfactomedin Propeller Selected From Invertebrate Phyla Reveal Cross-Talk with N-Terminal Blade and Surface Helices. Acta Crystallogr D Struct V. 75 817 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31478904
DOI: 10.1107/S205979831901074X