Calcium 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:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Structure of Human Ncs-1 Bound to Ric-8A, PDB code: 8alm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Structure of Human Ncs-1 Bound to Ric-8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca201 b:32.3 occ:1.00 OD1 B:ASP73 2.3 33.0 1.0 O B:ARG79 2.3 31.9 1.0 OD1 B:ASN75 2.4 37.3 1.0 OD1 B:ASP77 2.4 31.9 1.0 O B:HOH347 2.4 34.0 1.0 OE1 B:GLU84 2.5 31.1 1.0 OE2 B:GLU84 2.5 34.6 1.0 CD B:GLU84 2.8 27.3 1.0 CG B:ASP77 3.2 39.4 1.0 H B:ASP77 3.3 47.6 1.0 H B:ARG79 3.4 40.0 1.0 CG B:ASP73 3.4 28.3 1.0 CG B:ASN75 3.4 39.1 1.0 C B:ARG79 3.5 32.4 1.0 HA B:ASP73 3.5 34.2 1.0 H B:ASN75 3.6 47.3 1.0 HD21 B:ASN75 3.6 61.3 1.0 OD2 B:ASP77 3.6 40.9 1.0 HA B:ILE80 3.8 30.7 1.0 ND2 B:ASN75 3.9 50.9 1.0 H B:GLU81 4.0 38.1 1.0 HB2 B:ARG79 4.0 41.0 1.0 HG2 B:GLU81 4.1 50.3 1.0 N B:ARG79 4.1 33.2 1.0 N B:ASP77 4.2 39.5 1.0 CA B:ASP73 4.2 28.4 1.0 OD2 B:ASP73 4.2 32.1 1.0 H B:LYS76 4.2 42.0 1.0 CA B:ARG79 4.3 36.9 1.0 CB B:ASP73 4.3 30.0 1.0 N B:ASN75 4.3 39.2 1.0 CG B:GLU84 4.4 29.5 1.0 CB B:ASP77 4.4 39.5 1.0 N B:ILE80 4.4 27.7 1.0 H B:GLU74 4.4 40.6 1.0 C B:ASP73 4.5 31.4 1.0 CA B:ILE80 4.5 25.4 1.0 N B:LYS76 4.5 34.8 1.0 HB2 B:ASP73 4.5 36.2 1.0 H B:GLY78 4.6 41.3 1.0 HB3 B:ASP77 4.6 47.6 1.0 N B:GLU74 4.6 33.7 1.0 CB B:ARG79 4.6 34.0 1.0 N B:GLU81 4.6 31.6 1.0 CB B:ASN75 4.6 43.8 1.0 CA B:ASP77 4.7 41.9 1.0 HG3 B:GLU84 4.7 35.7 1.0 HB3 B:GLU81 4.7 47.4 1.0 HD22 B:ASN75 4.7 61.3 1.0 OE2 B:GLU81 4.8 58.6 1.0 HG2 B:GLU84 4.8 35.7 1.0 C B:ASN75 4.8 36.1 1.0 CA B:ASN75 4.8 45.4 1.0 N B:GLY78 4.8 34.2 1.0 HB3 B:ARG79 4.9 41.0 1.0 C B:ASP77 4.9 37.6 1.0 CG B:GLU81 4.9 41.8 1.0 HB2 B:GLU84 5.0 32.3 1.0 O B:ASP73 5.0 32.5 1.0 HB3 B:ASN75 5.0 52.7 1.0

Calcium binding site 2 out of 2 in the X-Ray Structure of Human Ncs-1 Bound to Ric-8A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human Ncs-1 Bound to Ric-8A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:30.1 occ:1.00 OD1 B:ASP111 2.3 34.8 1.0 O B:TYR115 2.3 28.6 1.0 O B:HOH366 2.4 33.4 1.0 OD1 B:ASP109 2.4 31.7 1.0 OD1 B:ASP113 2.4 31.6 1.0 OE1 B:GLU120 2.5 28.5 1.0 OE2 B:GLU120 2.5 32.9 1.0 CD B:GLU120 2.9 32.7 1.0 CG B:ASP111 3.3 37.3 1.0 CG B:ASP113 3.3 40.2 1.0 H B:ASP111 3.3 41.4 1.0 H B:ASP113 3.4 52.3 1.0 HA B:ASP109 3.4 33.7 1.0 CG B:ASP109 3.5 38.8 1.0 C B:TYR115 3.5 36.9 1.0 H B:TYR115 3.5 48.6 1.0 OD2 B:ASP113 3.7 41.4 1.0 OD2 B:ASP111 3.7 40.8 1.0 HA B:ILE116 3.8 38.9 1.0 H B:THR117 3.9 38.2 1.0 CA B:ASP109 4.1 27.9 1.0 N B:ASP111 4.1 34.3 1.0 H B:ASN112 4.2 43.9 1.0 N B:ASP113 4.2 43.4 1.0 H B:LEU110 4.2 39.4 1.0 N B:TYR115 4.2 40.3 1.0 HB2 B:TYR115 4.2 46.0 1.0 C B:ASP109 4.3 34.1 1.0 CB B:ASP109 4.3 30.6 1.0 OD2 B:ASP109 4.3 33.5 1.0 N B:LEU110 4.4 32.7 1.0 CB B:ASP113 4.4 38.3 1.0 CG B:GLU120 4.4 30.4 1.0 CA B:TYR115 4.4 37.3 1.0 HB3 B:ASP113 4.4 46.2 1.0 N B:ILE116 4.4 29.0 1.0 N B:ASN112 4.5 36.4 1.0 CB B:ASP111 4.5 39.5 1.0 CA B:ILE116 4.5 32.2 1.0 H B:GLY114 4.5 45.8 1.0 HB2 B:ASP109 4.6 37.0 1.0 N B:THR117 4.6 31.6 1.0 OG1 B:THR117 4.6 38.7 1.0 HG23 B:THR117 4.6 50.0 1.0 CA B:ASP111 4.6 40.0 1.0 HG3 B:GLU120 4.7 36.6 1.0 CA B:ASP113 4.7 48.9 1.0 C B:ASP111 4.7 33.3 1.0 HB3 B:ASP111 4.8 47.6 1.0 HG2 B:GLU120 4.8 36.6 1.0 N B:GLY114 4.8 38.0 1.0 CB B:TYR115 4.8 38.1 1.0 O B:ASP109 4.9 30.9 1.0 O B:HOH353 4.9 33.3 1.0 C B:ASP113 4.9 36.0 1.0 HG1 B:THR117 4.9 46.7 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