Sodium in PDB 8alm: X-Ray Structure of Human Ncs-1 Bound to Ric-8A

The structure of X-Ray Structure of Human Ncs-1 Bound to Ric-8A, PDB code: 8alm was solved by D.Munoz-Reyes, M.J.Sanchez-Barrena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.20 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.639, 56.639, 134.532, 90, 90, 90
R / Rfree (%)	21 / 25.3

The structure of X-Ray Structure of Human Ncs-1 Bound to Ric-8A also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of Human Ncs-1 Bound to Ric-8A (pdb code 8alm). 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 X-Ray Structure of Human Ncs-1 Bound to Ric-8A, PDB code: 8alm:

Sodium binding site 1 out of 1 in the X-Ray Structure of Human Ncs-1 Bound to Ric-8A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Human Ncs-1 Bound to Ric-8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:27.4 occ:1.00 O B:HOH314 2.1 41.4 1.0 OD1 B:ASP157 2.2 43.2 1.0 OD1 B:ASN159 2.3 43.0 1.0 OD1 B:ASP161 2.3 45.4 1.0 O B:LYS163 2.4 36.5 1.0 OE1 B:GLU168 2.4 46.5 1.0 OE2 B:GLU168 2.4 41.7 1.0 CD B:GLU168 2.7 41.5 1.0 CG B:ASP161 3.2 38.8 1.0 CG B:ASN159 3.3 56.5 1.0 CG B:ASP157 3.4 47.6 1.0 H B:ASP161 3.5 59.2 1.0 HD21 B:ASN159 3.5 62.1 1.0 OD2 B:ASP161 3.5 50.1 1.0 HA B:LEU164 3.6 39.0 1.0 HA B:ASP157 3.6 61.0 1.0 C B:LYS163 3.6 38.0 1.0 H B:LYS163 3.7 41.1 1.0 H B:ASN159 3.7 58.7 1.0 HD23 B:LEU164 3.8 54.3 1.0 ND2 B:ASN159 3.8 51.5 1.0 HG3 B:LYS163 3.9 50.2 1.0 OD2 B:ASP157 4.1 44.1 1.0 H B:THR165 4.2 45.2 1.0 CG B:GLU168 4.3 40.5 1.0 N B:ASP161 4.3 49.2 1.0 CA B:ASP157 4.3 50.7 1.0 H B:ALA160 4.4 67.7 1.0 HG23 B:THR165 4.4 62.1 1.0 O B:HOH321 4.4 51.5 1.0 CB B:ASP157 4.4 48.4 1.0 N B:LYS163 4.4 34.1 1.0 CB B:ASP161 4.4 44.7 1.0 CA B:LEU164 4.4 32.3 1.0 N B:LEU164 4.5 33.7 1.0 N B:ASN159 4.5 48.7 1.0 HG2 B:LYS163 4.5 50.2 1.0 HG3 B:GLU168 4.6 48.9 1.0 CA B:LYS163 4.6 32.1 1.0 HB3 B:ASP161 4.6 53.9 1.0 CB B:ASN159 4.6 53.8 1.0 CG B:LYS163 4.6 41.7 1.0 N B:ALA160 4.6 56.2 1.0 HD22 B:ASN159 4.7 62.1 1.0 HG2 B:GLU168 4.7 48.9 1.0 CD2 B:LEU164 4.7 45.0 1.0 C B:ASP157 4.7 47.0 1.0 HB2 B:ASP157 4.8 58.3 1.0 H B:LYS158 4.8 66.3 1.0 CA B:ASP161 4.8 48.4 1.0 C B:ASN159 4.9 56.0 1.0 CA B:ASN159 4.9 61.6 1.0 N B:THR165 4.9 37.5 1.0 HD22 B:LEU164 4.9 54.3 1.0 N B:LYS158 4.9 55.1 1.0 H B:GLY162 4.9 54.6 1.0 HB3 B:ASN159 5.0 64.8 1.0 HB2 B:GLU168 5.0 50.4 1.0

D.Munoz-Reyes, L.J.Mcclelland, S.Arroyo-Urea, S.Sanchez-Yepes, J.Sabin, S.Perez-Suarez, M.Menendez, A.Mansilla, J.Garcia-Nafria, S.Sprang, M.J.Sanchez-Barrena. The Neuronal Calcium Sensor Ncs-1 Regulates the Phosphorylation State and Activity of the Ga Chaperone and Gef Ric-8A. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 38018500
DOI: 10.7554/ELIFE.86151