Sodium in PDB 8alh: 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: 8alh 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)	52.38 / 1.86
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.861, 56.861, 134.612, 90, 90, 90
R / Rfree (%)	19.6 / 23.1

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

Calcium	(Ca)	2 atoms
Magnesium	(Mg)	1 atom
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 8alh). 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: 8alh:

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:21.7 occ:1.00 O B:HOH309 2.0 37.3 1.0 O B:LYS163 2.3 29.1 1.0 OD1 B:ASP157 2.3 39.7 1.0 OD1 B:ASN159 2.4 44.7 1.0 OE1 B:GLU168 2.4 35.9 1.0 OD1 B:ASP161 2.4 44.3 1.0 OE2 B:GLU168 2.5 35.1 1.0 CD B:GLU168 2.8 33.7 1.0 CG B:ASP161 3.3 37.0 1.0 CG B:ASN159 3.4 52.6 1.0 HD21 B:ASN159 3.4 60.9 1.0 HA B:LEU164 3.5 35.2 1.0 OD2 B:ASP161 3.5 44.4 1.0 CG B:ASP157 3.5 38.7 1.0 C B:LYS163 3.5 30.1 1.0 H B:LYS163 3.6 35.7 1.0 H B:ASP161 3.6 48.6 1.0 HA B:ASP157 3.7 46.8 1.0 ND2 B:ASN159 3.8 50.8 1.0 H B:ASN159 3.9 57.3 1.0 HD23 B:LEU164 3.9 40.9 1.0 HG3 B:LYS163 4.0 39.7 1.0 H B:THR165 4.0 36.6 1.0 OD2 B:ASP157 4.2 39.8 1.0 HG2 B:LYS163 4.3 39.7 1.0 HG23 B:THR165 4.3 50.2 1.0 CG B:GLU168 4.3 32.5 1.0 CA B:LEU164 4.3 29.3 1.0 N B:LEU164 4.4 26.4 1.0 N B:LYS163 4.4 29.8 1.0 CA B:ASP157 4.4 39.0 1.0 N B:ASP161 4.5 40.5 1.0 HZ2 B:LYS163 4.5 85.5 1.0 O B:HOH343 4.5 46.1 1.0 H B:ALA160 4.5 65.0 1.0 CA B:LYS163 4.5 29.9 1.0 CB B:ASP157 4.5 47.0 1.0 CG B:LYS163 4.5 33.1 1.0 CB B:ASP161 4.5 44.8 1.0 HG3 B:GLU168 4.6 39.1 1.0 HD22 B:ASN159 4.6 60.9 1.0 N B:ASN159 4.6 47.8 1.0 N B:THR165 4.7 30.5 1.0 CB B:ASN159 4.7 51.5 1.0 H B:LYS158 4.7 57.4 1.0 HG2 B:GLU168 4.7 39.1 1.0 HB3 B:ASP161 4.8 53.7 1.0 N B:ALA160 4.8 54.2 1.0 C B:ASP157 4.8 40.2 1.0 CD2 B:LEU164 4.9 34.0 1.0 HB2 B:ASP157 4.9 56.3 1.0 HB2 B:GLU168 4.9 35.6 1.0 H B:GLY162 4.9 48.2 1.0 N B:LYS158 4.9 47.8 1.0 CA B:ASP161 5.0 40.0 1.0 C B:LEU164 5.0 28.3 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