Calcium 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
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 8ahy). 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: 8ahy:
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:23.2 occ:1.00 O B:ARG79 2.2 25.3 1.0 OD1 B:ASN75 2.4 28.1 1.0 OD1 B:ASP73 2.4 22.6 1.0 OE1 B:GLU84 2.4 23.9 1.0 OE2 B:GLU84 2.5 24.4 1.0 OD1 B:ASP77 2.5 26.2 1.0 OE1 B:GLU81 2.5 39.6 1.0 CD B:GLU84 2.8 23.7 1.0 CG B:ASP77 3.3 33.7 1.0 CG B:ASN75 3.4 33.0 1.0 H B:ASP77 3.4 34.0 1.0 C B:ARG79 3.5 22.8 1.0 CD B:GLU81 3.5 51.5 1.0 HA B:ASP73 3.5 29.2 1.0 H B:ARG79 3.5 28.5 1.0 CG B:ASP73 3.5 24.1 1.0 H B:ASN75 3.6 39.8 1.0 H B:GLU81 3.6 31.4 1.0 HD21 B:ASN75 3.6 42.9 1.0 OD2 B:ASP77 3.6 33.2 1.0 HA B:ILE80 3.7 22.8 1.0 OE2 B:GLU81 3.7 55.1 1.0 ND2 B:ASN75 3.9 35.8 1.0 HB2 B:ARG79 4.1 30.1 1.0 CA B:ASP73 4.2 24.3 1.0 N B:ASP77 4.2 28.4 1.0 N B:ARG79 4.3 23.8 1.0 H B:LYS76 4.3 31.8 1.0 CG B:GLU84 4.3 26.1 1.0 H B:GLU74 4.3 32.8 1.0 N B:ASN75 4.3 33.2 1.0 N B:ILE80 4.4 24.3 1.0 OD2 B:ASP73 4.4 24.9 1.0 N B:GLU81 4.4 26.2 1.0 CA B:ARG79 4.4 23.1 1.0 CB B:ASP73 4.4 21.9 1.0 CA B:ILE80 4.4 18.9 1.0 C B:ASP73 4.4 23.9 1.0 CB B:ASP77 4.5 29.7 1.0 N B:GLU74 4.5 27.3 1.0 N B:LYS76 4.5 26.5 1.0 HB2 B:GLU81 4.6 32.9 1.0 HG3 B:GLU84 4.6 31.3 1.0 CB B:ASN75 4.6 32.8 1.0 HB2 B:ASP73 4.6 26.3 1.0 HB3 B:ASP77 4.6 35.7 1.0 HG2 B:GLU84 4.7 31.3 1.0 CB B:ARG79 4.7 25.1 1.0 HD22 B:ASN75 4.7 42.9 1.0 H B:GLY78 4.8 28.9 1.0 C B:ASN75 4.8 30.2 1.0 CA B:ASN75 4.8 31.3 1.0 CA B:ASP77 4.8 29.4 1.0 HB2 B:GLU84 4.9 22.7 1.0 CG B:GLU81 4.9 42.3 1.0 C B:ILE80 4.9 24.0 1.0 O B:HOH359 4.9 35.7 1.0 N B:GLY78 5.0 24.1 1.0 HB3 B:ARG79 5.0 30.1 1.0 HB3 B:ASN75 5.0 39.3 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:18.9 occ:1.00 O B:TYR115 2.3 21.7 1.0 OD1 B:ASP111 2.4 20.5 1.0 O B:HOH384 2.4 22.6 1.0 OD1 B:ASP109 2.4 20.4 1.0 OD1 B:ASP113 2.5 22.9 1.0 OE2 B:GLU120 2.5 21.9 1.0 OE1 B:GLU120 2.5 18.7 1.0 CD B:GLU120 2.8 20.8 1.0 CG B:ASP111 3.3 19.2 1.0 CG B:ASP113 3.3 23.8 1.0 HA B:ASP109 3.3 25.9 1.0 H B:ASP113 3.4 27.2 1.0 H B:ASP111 3.4 23.3 1.0 H B:TYR115 3.5 23.7 1.0 C B:TYR115 3.5 20.5 1.0 CG B:ASP109 3.5 22.4 1.0 OD2 B:ASP111 3.7 21.4 1.0 HA B:ILE116 3.7 20.9 1.0 OD2 B:ASP113 3.8 27.4 1.0 H B:THR117 3.9 20.9 1.0 CA B:ASP109 4.0 21.6 1.0 N B:TYR115 4.2 19.7 1.0 HB2 B:TYR115 4.2 25.1 1.0 N B:ASP113 4.2 22.7 1.0 H B:ASN112 4.2 24.8 1.0 N B:ASP111 4.2 19.4 1.0 H B:LEU110 4.2 24.4 1.0 C B:ASP109 4.3 21.5 1.0 CB B:ASP109 4.3 18.0 1.0 CG B:GLU120 4.3 22.2 1.0 OD2 B:ASP109 4.3 19.9 1.0 CA B:TYR115 4.4 17.8 1.0 N B:ILE116 4.4 19.5 1.0 CB B:ASP113 4.4 23.3 1.0 CA B:ILE116 4.4 17.4 1.0 N B:LEU110 4.4 20.3 1.0 CB B:ASP111 4.5 23.2 1.0 HB3 B:ASP113 4.5 28.0 1.0 HG23 B:THR117 4.5 25.9 1.0 H B:GLY114 4.5 25.3 1.0 HB2 B:ASP109 4.5 21.6 1.0 N B:THR117 4.6 17.4 1.0 N B:ASN112 4.6 20.7 1.0 OG1 B:THR117 4.6 22.6 1.0 HG3 B:GLU120 4.6 26.6 1.0 CA B:ASP113 4.7 24.8 1.0 CA B:ASP111 4.7 20.0 1.0 HB3 B:ASP111 4.8 27.9 1.0 HG2 B:GLU120 4.8 26.6 1.0 O B:HOH356 4.8 31.6 1.0 CB B:TYR115 4.8 20.9 1.0 N B:GLY114 4.8 21.1 1.0 C B:ASP111 4.8 23.2 1.0 O B:ASP109 4.8 20.1 1.0 C B:ILE116 4.9 18.8 1.0 C B:ASP113 5.0 22.0 1.0 HG1 B:THR117 5.0 27.2 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