Sodium in PDB 8ahy: 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: 8ahy 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)	52.24 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.635, 56.635, 135.297, 90, 90, 90
R / Rfree (%)	18.6 / 20.8

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

Magnesium	(Mg)	1 atom
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 8ahy). 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: 8ahy:

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:16.6 occ:1.00 OD1 B:ASP157 2.2 28.6 1.0 O B:HOH318 2.2 30.5 1.0 O B:LYS163 2.3 25.2 1.0 OD1 B:ASP161 2.3 34.3 1.0 OD1 B:ASN159 2.3 30.5 1.0 OE1 B:GLU168 2.4 29.4 1.0 OE2 B:GLU168 2.6 30.2 1.0 CD B:GLU168 2.8 30.7 1.0 CG B:ASP161 3.2 30.2 1.0 CG B:ASN159 3.4 34.9 1.0 CG B:ASP157 3.4 26.1 1.0 H B:ASP161 3.5 40.0 1.0 HA B:LEU164 3.5 26.5 1.0 HA B:ASP157 3.5 37.2 1.0 C B:LYS163 3.5 26.1 1.0 HD21 B:ASN159 3.6 44.1 1.0 OD2 B:ASP161 3.6 37.2 1.0 H B:LYS163 3.6 26.5 1.0 H B:ASN159 3.8 41.3 1.0 ND2 B:ASN159 3.9 36.7 1.0 HD23 B:LEU164 3.9 32.9 1.0 H B:THR165 4.2 27.7 1.0 OD2 B:ASP157 4.2 29.6 1.0 CA B:ASP157 4.3 31.0 1.0 HG2 B:LYS163 4.3 32.1 1.0 HG3 B:LYS163 4.3 32.1 1.0 N B:ASP161 4.3 33.3 1.0 CA B:LEU164 4.3 22.1 1.0 H B:ALA160 4.4 43.8 1.0 CG B:GLU168 4.4 29.4 1.0 N B:LYS163 4.4 22.1 1.0 N B:LEU164 4.4 21.9 1.0 CB B:ASP157 4.4 29.4 1.0 HG23 B:THR165 4.5 36.4 1.0 CB B:ASP161 4.5 34.6 1.0 H B:LYS158 4.5 44.8 1.0 N B:ASN159 4.5 34.4 1.0 CA B:LYS163 4.5 22.1 1.0 O B:HOH326 4.6 36.4 1.0 N B:ALA160 4.6 36.5 1.0 C B:ASP157 4.7 31.8 1.0 CB B:ASN159 4.7 40.4 1.0 HB3 B:ASP161 4.7 41.5 1.0 CG B:LYS163 4.7 26.8 1.0 HG3 B:GLU168 4.7 35.3 1.0 HD22 B:ASN159 4.7 44.1 1.0 N B:LYS158 4.7 37.3 1.0 H B:GLY162 4.7 30.7 1.0 HB2 B:ASP157 4.8 35.2 1.0 HG2 B:GLU168 4.8 35.3 1.0 CD2 B:LEU164 4.8 27.4 1.0 N B:THR165 4.8 23.1 1.0 CA B:ASP161 4.8 30.1 1.0 C B:ASN159 4.9 35.9 1.0 CA B:ASN159 4.9 35.0 1.0 HZ1 B:LYS163 5.0 68.9 1.0 HB2 B:GLU168 5.0 33.4 1.0 HD22 B:LEU164 5.0 32.9 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