Sodium in PDB 4zdm: Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex

The structure of Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex, PDB code: 4zdm was solved by R.J.Grey, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.38 / 1.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	159.850, 159.850, 55.614, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.7

The binding sites of Sodium atom in the Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex (pdb code 4zdm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex, PDB code: 4zdm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:36.5 occ:0.73 OE2 A:GLU150 2.3 33.0 0.7 OD1 A:ASP145 2.4 27.4 1.0 O A:HOH698 2.6 47.7 1.0 HG3 A:LYS170 2.8 27.1 1.0 O A:HOH682 3.1 54.8 1.0 HB2 A:ASP145 3.2 20.2 1.0 HA A:ASP145 3.3 18.4 1.0 CD A:GLU150 3.3 31.5 0.7 O A:HOH413 3.4 44.3 1.0 CG A:ASP145 3.4 21.2 1.0 HE2 A:LYS170 3.4 25.1 1.0 HB3 A:LYS170 3.4 26.6 1.0 HD2 A:LYS170 3.5 22.9 1.0 OE1 A:GLU150 3.6 33.4 0.7 CG A:LYS170 3.6 22.5 1.0 CB A:ASP145 3.6 16.8 1.0 HG3 A:GLU150 3.8 27.8 0.3 CD A:LYS170 3.9 19.1 1.0 CA A:ASP145 4.0 15.3 1.0 CB A:LYS170 4.0 22.1 1.0 CE A:LYS170 4.1 20.9 1.0 H A:SER146 4.3 15.7 1.0 HG2 A:LYS170 4.4 27.1 1.0 HB2 A:LYS170 4.4 26.6 1.0 O A:HOH742 4.5 43.0 1.0 OD2 A:ASP145 4.5 24.1 1.0 HB3 A:ASP145 4.6 20.2 1.0 HE3 A:LYS170 4.6 25.1 1.0 CG A:GLU150 4.7 23.1 0.3 CG A:GLU150 4.7 19.9 0.7 O A:HOH798 4.7 48.7 1.0 HG3 A:GLU150 4.7 23.9 0.7 CD A:GLU150 4.8 32.9 0.3 HD3 A:LYS170 4.8 22.9 1.0 N A:SER146 4.9 13.1 1.0 N A:ASP145 4.9 12.4 1.0 OE2 A:GLU150 4.9 31.2 0.3 C A:ASP145 5.0 12.1 1.0

Sodium binding site 2 out of 2 in the Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pleurobrachia Bachei IGLUR3 Lbd Glycine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:44.5 occ:1.00 O A:HOH660 2.2 40.9 1.0 OD1 A:ASP160 2.2 30.4 1.0 HA A:ASP160 2.5 35.1 1.0 HD13 A:LEU134 3.2 30.9 1.0 CG A:ASP160 3.3 44.0 1.0 CA A:ASP160 3.4 29.3 1.0 HB2 A:ARG163 3.4 30.8 1.0 HB3 A:ARG163 3.4 30.8 1.0 CB A:ASP160 3.7 35.1 1.0 HG2 A:ARG163 3.8 38.5 1.0 CB A:ARG163 3.8 25.7 1.0 HD3 A:ARG163 3.8 37.5 1.0 N A:ASP160 3.9 24.7 1.0 HB3 A:ASP160 3.9 42.2 1.0 CD1 A:LEU134 3.9 25.8 1.0 O A:ALA159 4.0 22.0 1.0 HD11 A:LEU134 4.0 30.9 1.0 HH11 A:ARG163 4.1 27.7 1.0 CG A:ARG163 4.2 32.1 1.0 C A:ALA159 4.2 23.5 1.0 HD12 A:LEU134 4.2 30.9 1.0 O A:HOH678 4.3 41.6 1.0 OD2 A:ASP160 4.4 51.7 1.0 H A:ASP160 4.4 29.6 1.0 CD A:ARG163 4.5 31.3 1.0 C A:ASP160 4.5 22.2 1.0 O A:ASP160 4.6 22.1 1.0 HB2 A:ASP160 4.7 42.2 1.0 H A:ARG163 4.8 24.6 1.0 HD22 A:LEU134 4.8 31.9 1.0 HB3 A:ALA159 4.9 33.5 1.0 HB1 A:ALA159 4.9 33.5 1.0 NH1 A:ARG163 4.9 23.1 1.0

R.Alberstein, R.Grey, A.Zimmet, D.K.Simmons, M.L.Mayer. Glycine Activated Ion Channel Subunits Encoded By Ctenophore Glutamate Receptor Genes. Proc.Natl.Acad.Sci.Usa V. 112 E6048 2015.
ISSN: ESSN 1091-6490
PubMed: 26460032
DOI: 10.1073/PNAS.1513771112