Calcium in PDB 5g08: Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine

The structure of Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine, PDB code: 5g08 was solved by A.Chaves-Sanjuan, L.Infantes, M.J.Sanchez-Barrena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.217, 54.917, 60.210, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.6

The structure of Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine (pdb code 5g08). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine, PDB code: 5g08:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1184 b:32.4 occ:1.00 O A:ALA79 2.2 31.6 1.0 OD1 A:ASP73 2.3 32.0 1.0 O A:HOH2090 2.3 43.0 1.0 OE1 A:GLU84 2.4 31.1 1.0 OD1 A:ASN75 2.4 37.4 1.0 OD1 A:ASP77 2.4 34.6 1.0 OE2 A:GLU84 2.5 29.9 1.0 CD A:GLU84 2.8 29.7 1.0 CG A:ASP77 3.4 37.1 1.0 CG A:ASN75 3.4 41.7 1.0 CG A:ASP73 3.4 29.2 1.0 C A:ALA79 3.5 28.3 1.0 OD2 A:ASP77 3.8 40.9 1.0 ND2 A:ASN75 3.8 48.3 1.0 CA A:ASP73 4.1 24.8 1.0 N A:ALA79 4.2 31.7 1.0 CB A:ASP73 4.2 25.7 1.0 OD2 A:ASP73 4.3 29.5 1.0 CG A:GLU84 4.3 27.9 1.0 OE2 A:GLU81 4.3 67.3 1.0 N A:ASP77 4.3 34.4 1.0 CG A:GLU81 4.3 52.4 1.0 CA A:ILE80 4.3 29.9 1.0 N A:ILE80 4.4 27.2 1.0 CA A:ALA79 4.4 30.0 1.0 N A:ASN75 4.4 35.0 1.0 N A:GLU81 4.4 28.9 1.0 C A:ASP73 4.4 31.1 1.0 CB A:ASP77 4.5 40.2 1.0 N A:GLU74 4.6 26.6 1.0 CB A:ASN75 4.7 36.9 1.0 CD A:GLU81 4.7 64.4 1.0 N A:ASN76 4.7 38.4 1.0 O A:HOH2096 4.8 42.9 1.0 CA A:ASP77 4.8 40.2 1.0 CA A:ASN75 4.9 40.9 1.0 C A:ILE80 4.9 26.6 1.0 C A:ASN75 4.9 38.5 1.0 N A:GLY78 4.9 35.9 1.0 CB A:ALA79 5.0 34.7 1.0 O A:ASP73 5.0 28.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1185 b:27.9 occ:1.00 O A:HOH2139 2.3 33.2 1.0 O A:ARG162 2.3 31.1 1.0 OD1 A:ASN158 2.3 30.3 1.0 OE1 A:GLU167 2.4 26.8 1.0 OD1 A:ASP156 2.4 30.3 1.0 OD1 A:ASP160 2.4 34.2 1.0 OE2 A:GLU167 2.4 29.1 1.0 CD A:GLU167 2.7 30.5 1.0 CG A:ASP160 3.3 37.4 1.0 CG A:ASN158 3.5 43.0 1.0 CG A:ASP156 3.5 31.5 1.0 C A:ARG162 3.6 31.4 1.0 OD2 A:ASP160 3.7 37.2 1.0 ND2 A:ASN158 4.0 44.8 1.0 CG A:GLU167 4.3 28.8 1.0 N A:ARG162 4.3 31.3 1.0 N A:ASP160 4.3 37.4 1.0 CA A:ASP156 4.3 29.1 1.0 OD2 A:ASP156 4.3 34.6 1.0 N A:ASN158 4.4 36.7 1.0 CA A:LEU163 4.4 27.6 1.0 N A:LEU163 4.4 27.6 1.0 CB A:ASP156 4.4 33.5 1.0 CA A:ARG162 4.5 30.4 1.0 C A:ASP156 4.5 33.9 1.0 CB A:ASP160 4.5 34.0 1.0 N A:LYS157 4.6 33.4 1.0 N A:HIS159 4.6 38.2 1.0 O A:HOH2140 4.7 36.9 1.0 CG A:ARG162 4.7 37.0 1.0 CB A:ASN158 4.7 41.1 1.0 O A:HOH2138 4.7 35.6 1.0 N A:THR164 4.8 24.1 1.0 CA A:ASP160 4.8 36.1 1.0 C A:ASN158 4.8 43.8 1.0 CA A:ASN158 4.9 36.9 1.0 CD2 A:LEU163 4.9 26.9 1.0 O A:HOH2068 5.0 36.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Drosophila Ncs-1 Bound to Chlorpromazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1186 b:27.9 occ:1.00 O A:TYR115 2.3 30.9 1.0 O A:HOH2114 2.3 34.2 1.0 OD1 A:ASP111 2.4 34.1 1.0 OD1 A:ASP109 2.4 27.8 1.0 OE2 A:GLU120 2.4 30.9 1.0 OD1 A:ASP113 2.4 27.3 1.0 OE1 A:GLU120 2.5 30.1 1.0 CD A:GLU120 2.8 28.6 1.0 CG A:ASP113 3.3 29.9 1.0 CG A:ASP111 3.3 34.2 1.0 CG A:ASP109 3.5 24.1 1.0 C A:TYR115 3.5 24.5 1.0 OD2 A:ASP111 3.8 41.4 1.0 OD2 A:ASP113 3.8 32.3 1.0 CA A:ASP109 4.1 23.7 1.0 N A:ASP113 4.2 30.0 1.0 N A:TYR115 4.2 21.9 1.0 N A:ASP111 4.2 33.8 1.0 CG A:GLU120 4.2 26.5 1.0 OD2 A:ASP109 4.3 25.7 1.0 CB A:ASP109 4.3 22.0 1.0 C A:ASP109 4.3 26.5 1.0 CB A:ASP113 4.4 31.1 1.0 CA A:TYR115 4.4 23.8 1.0 N A:ILE116 4.4 26.1 1.0 N A:VAL110 4.5 28.7 1.0 CA A:ILE116 4.5 23.4 1.0 N A:ASN112 4.6 29.3 1.0 CB A:ASP111 4.6 36.3 1.0 CB A:TYR115 4.7 25.7 1.0 CA A:ASP113 4.7 30.5 1.0 CA A:ASP111 4.7 33.6 1.0 N A:THR117 4.7 28.1 1.0 CG2 A:THR117 4.7 34.6 1.0 C A:ASP111 4.8 33.5 1.0 O A:ASP109 4.9 26.1 1.0 O A:HOH2115 4.9 43.8 1.0 N A:GLY114 5.0 27.2 1.0

A.Mansilla, A.Chaves-Sanjuan, N.E.Campillo, O.Semelidou, L.Martinez-Gonzalez, L.Infantes, J.M.Gonzalez-Rubio, C.Gil, S.Conde, E.M.Skoulakis, A.Ferrus, A.Martinez, M.J.Sanchez-Barrena. Interference of the Complex Between Ncs-1 and RIC8A with Phenothiazines Regulates Synaptic Function and Is An Approach For Fragile X Syndrome. Proc. Natl. Acad. Sci. V. 114 E999 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28119500
DOI: 10.1073/PNAS.1611089114