Calcium 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:

Magnesium	(Mg)	1 atom
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 8alh). 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: 8alh:
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:28.6 occ:1.00 O B:ARG79 2.3 26.9 1.0 O B:HOH352 2.3 35.5 1.0 OD1 B:ASN75 2.3 33.2 1.0 OD1 B:ASP73 2.3 30.9 1.0 OE2 B:GLU84 2.4 28.6 1.0 OD1 B:ASP77 2.5 28.7 1.0 OE1 B:GLU84 2.5 26.3 1.0 CD B:GLU84 2.8 27.2 1.0 CG B:ASP77 3.2 37.0 1.0 CG B:ASN75 3.3 40.4 1.0 H B:ASP77 3.4 39.2 1.0 C B:ARG79 3.5 24.6 1.0 H B:ARG79 3.5 35.4 1.0 CG B:ASP73 3.5 25.2 1.0 HD21 B:ASN75 3.5 44.8 1.0 HA B:ASP73 3.6 33.8 1.0 OD2 B:ASP77 3.6 37.9 1.0 H B:ASN75 3.6 40.8 1.0 H B:GLU81 3.8 30.4 1.0 HA B:ILE80 3.8 31.8 1.0 ND2 B:ASN75 3.8 37.3 1.0 HB2 B:ARG79 4.1 38.0 1.0 H B:LYS76 4.1 41.2 1.0 N B:ARG79 4.2 29.5 1.0 CA B:ASP73 4.2 28.1 1.0 HG2 B:GLU81 4.2 50.1 1.0 N B:ASP77 4.2 32.7 1.0 H B:GLU74 4.2 36.2 1.0 OD2 B:ASP73 4.3 32.0 1.0 N B:ASN75 4.3 34.0 1.0 CG B:GLU84 4.3 25.5 1.0 CA B:ARG79 4.4 32.9 1.0 CB B:ASP73 4.4 23.9 1.0 N B:ILE80 4.4 23.5 1.0 C B:ASP73 4.4 27.0 1.0 CB B:ASP77 4.4 34.5 1.0 N B:GLU74 4.5 30.1 1.0 N B:LYS76 4.5 34.3 1.0 CA B:ILE80 4.5 26.5 1.0 N B:GLU81 4.5 25.3 1.0 CB B:ASN75 4.6 38.0 1.0 HB3 B:ASP77 4.6 41.4 1.0 HB2 B:ASP73 4.6 28.7 1.0 H B:GLY78 4.6 38.4 1.0 HD22 B:ASN75 4.7 44.8 1.0 OE2 B:GLU81 4.7 64.9 1.0 HG3 B:GLU84 4.7 30.6 1.0 HB3 B:GLU81 4.7 37.2 1.0 CB B:ARG79 4.7 31.6 1.0 HG2 B:GLU84 4.8 30.6 1.0 C B:ASN75 4.8 37.4 1.0 CA B:ASP77 4.8 38.2 1.0 CA B:ASN75 4.8 36.2 1.0 N B:GLY78 4.9 32.0 1.0 HB2 B:GLU84 4.9 28.3 1.0 O B:HOH380 5.0 40.5 1.0 HB3 B:ASN75 5.0 45.6 1.0 HB3 B:ARG79 5.0 38.0 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:22.1 occ:1.00 O B:TYR115 2.2 24.6 1.0 OD1 B:ASP111 2.3 25.5 1.0 OD1 B:ASP109 2.3 24.9 1.0 O B:HOH372 2.4 25.0 1.0 OE1 B:GLU120 2.5 22.0 1.0 OE2 B:GLU120 2.5 23.1 1.0 OD1 B:ASP113 2.5 25.0 1.0 CD B:GLU120 2.8 27.3 1.0 CG B:ASP111 3.2 20.9 1.0 HA B:ASP109 3.3 26.8 1.0 CG B:ASP113 3.3 28.2 1.0 H B:ASP113 3.4 30.6 1.0 H B:TYR115 3.4 26.6 1.0 H B:ASP111 3.4 27.6 1.0 C B:TYR115 3.4 25.4 1.0 CG B:ASP109 3.5 25.8 1.0 OD2 B:ASP111 3.6 22.1 1.0 HA B:ILE116 3.7 30.1 1.0 OD2 B:ASP113 3.8 28.7 1.0 H B:THR117 3.9 28.5 1.0 CA B:ASP109 4.0 22.3 1.0 N B:TYR115 4.1 22.1 1.0 HB2 B:TYR115 4.2 36.8 1.0 N B:ASP113 4.2 25.5 1.0 H B:LEU110 4.2 28.2 1.0 N B:ASP111 4.2 23.0 1.0 H B:ASN112 4.2 29.0 1.0 CB B:ASP109 4.2 23.3 1.0 C B:ASP109 4.3 20.2 1.0 CA B:TYR115 4.3 25.4 1.0 CG B:GLU120 4.3 24.7 1.0 N B:ILE116 4.4 27.1 1.0 OD2 B:ASP109 4.4 24.0 1.0 N B:LEU110 4.4 23.5 1.0 CB B:ASP113 4.4 30.2 1.0 HB2 B:ASP109 4.4 28.0 1.0 CA B:ILE116 4.4 25.1 1.0 CB B:ASP111 4.5 27.6 1.0 HB3 B:ASP113 4.5 36.3 1.0 N B:THR117 4.5 23.7 1.0 HG23 B:THR117 4.6 35.1 1.0 N B:ASN112 4.6 24.1 1.0 OG1 B:THR117 4.6 28.8 1.0 H B:GLY114 4.6 32.7 1.0 HG3 B:GLU120 4.6 29.7 1.0 O B:HOH333 4.7 38.0 1.0 CA B:ASP113 4.7 32.1 1.0 CA B:ASP111 4.7 28.0 1.0 HB3 B:ASP111 4.7 33.1 1.0 HG2 B:GLU120 4.7 29.7 1.0 CB B:TYR115 4.8 30.7 1.0 C B:ASP111 4.8 29.3 1.0 N B:GLY114 4.8 27.2 1.0 O B:ASP109 4.9 24.4 1.0 C B:ILE116 4.9 22.4 1.0 C B:ASP113 4.9 28.9 1.0 HG1 B:THR117 4.9 34.6 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