Calcium in PDB 5fyx: Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16

The structure of Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16, PDB code: 5fyx was solved by L.Martinez-Gonzalez, 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)	44.70 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.057, 62.997, 63.425, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25.2

The structure of Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16 (pdb code 5fyx). 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 Penothiazine FD16, PDB code: 5fyx:
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 Penothiazine FD16


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 Penothiazine FD16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1186 b:30.6 occ:1.00 OD1 A:ASN75 2.2 38.3 1.0 O A:ALA79 2.2 30.9 1.0 OD1 A:ASP73 2.3 37.7 1.0 O A:HOH2050 2.4 44.9 1.0 OE1 A:GLU84 2.4 33.9 1.0 OD1 A:ASP77 2.5 30.6 1.0 OE2 A:GLU84 2.6 30.6 1.0 CD A:GLU84 2.8 44.4 1.0 CG A:ASP77 3.2 35.5 1.0 CG A:ASN75 3.3 40.7 1.0 OD2 A:ASP77 3.4 37.4 1.0 C A:ALA79 3.4 30.6 1.0 CG A:ASP73 3.5 35.4 1.0 ND2 A:ASN75 3.8 46.7 1.0 N A:ALA79 4.2 34.5 1.0 CA A:ASP73 4.3 40.4 1.0 OD2 A:ASP73 4.3 40.4 1.0 N A:ASP77 4.3 43.2 1.0 CG A:GLU84 4.3 34.3 1.0 CA A:ALA79 4.3 30.6 1.0 N A:ILE80 4.4 30.6 1.0 CB A:ASP73 4.4 39.4 1.0 CA A:ILE80 4.4 30.6 1.0 N A:ASN75 4.4 43.9 1.0 OE2 A:GLU81 4.4 63.4 1.0 CB A:ASP77 4.5 39.0 1.0 CB A:ASN75 4.5 36.2 1.0 N A:GLU81 4.5 30.6 1.0 C A:ASP73 4.6 42.6 1.0 O A:HOH2053 4.6 57.3 1.0 CG A:GLU81 4.6 58.5 1.0 N A:ASN76 4.7 39.3 1.0 N A:GLU74 4.7 43.5 1.0 CB A:ALA79 4.7 30.6 1.0 CA A:ASN75 4.8 41.9 1.0 CA A:ASP77 4.9 36.4 1.0 C A:ASN75 4.9 39.2 1.0 N A:GLY78 5.0 30.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16


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 Penothiazine FD16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1187 b:52.7 occ:1.00 OE1 A:GLU167 2.3 56.5 1.0 OD1 A:ASP156 2.3 50.3 1.0 O A:HOH2073 2.4 51.6 1.0 O A:ARG162 2.4 47.7 1.0 OD1 A:ASP160 2.5 53.8 1.0 OE2 A:GLU167 2.6 50.6 1.0 CD A:GLU167 2.8 56.4 1.0 OD1 A:ASN158 2.9 74.7 1.0 CG A:ASP160 3.3 53.0 1.0 OD2 A:ASP160 3.5 55.9 1.0 C A:ARG162 3.5 45.9 1.0 CG A:ASP156 3.5 48.6 1.0 CG A:ASN158 3.6 68.7 1.0 ND2 A:ASN158 3.9 64.2 1.0 N A:ARG162 4.2 48.5 1.0 CA A:ASP156 4.3 54.1 1.0 CA A:ARG162 4.3 44.0 1.0 CG A:GLU167 4.3 50.2 1.0 OD2 A:ASP156 4.3 49.0 1.0 N A:ASP160 4.4 59.7 1.0 CB A:ASP156 4.4 51.4 1.0 N A:LEU163 4.4 43.7 1.0 CA A:LEU163 4.4 45.0 1.0 N A:LYS157 4.5 54.4 1.0 CB A:ARG162 4.5 45.5 1.0 N A:ASN158 4.5 65.1 1.0 C A:ASP156 4.5 60.8 1.0 CB A:ASP160 4.6 54.1 1.0 N A:HIS159 4.7 64.1 1.0 N A:THR164 4.8 42.0 1.0 CA A:ASP160 4.9 55.3 1.0 CB A:ASN158 4.9 73.0 1.0 CD2 A:LEU163 4.9 45.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD16


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 Penothiazine FD16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1188 b:68.0 occ:1.00 OE2 A:GLU120 2.4 48.5 1.0 OE1 A:GLU120 2.4 49.6 1.0 OD1 A:ASP111 2.5 40.9 1.0 OD1 A:ASP113 2.5 48.8 1.0 O A:TYR115 2.5 36.3 1.0 OD1 A:ASP109 2.5 44.4 1.0 O A:HOH2063 2.5 49.6 1.0 CD A:GLU120 2.7 50.6 1.0 CG A:ASP111 3.3 55.2 1.0 CG A:ASP113 3.3 53.2 1.0 CG A:ASP109 3.6 47.6 1.0 OD2 A:ASP111 3.6 56.4 1.0 C A:TYR115 3.7 44.6 1.0 OD2 A:ASP113 3.7 49.2 1.0 CA A:ASP109 4.1 46.8 1.0 N A:ASP111 4.2 48.6 1.0 CG A:GLU120 4.2 47.3 1.0 N A:ASP113 4.3 48.3 1.0 N A:VAL110 4.4 49.9 1.0 C A:ASP109 4.4 48.1 1.0 OD2 A:ASP109 4.4 44.7 1.0 CB A:ASP109 4.4 42.4 1.0 N A:TYR115 4.4 44.7 1.0 CB A:ASP113 4.5 48.2 1.0 CA A:TYR115 4.5 44.8 1.0 CB A:ASP111 4.6 42.9 1.0 N A:ASN112 4.6 53.8 1.0 N A:ILE116 4.6 44.3 1.0 CA A:ILE116 4.6 37.4 1.0 O A:HOH2062 4.6 48.5 1.0 CA A:ASP111 4.7 50.8 1.0 N A:THR117 4.8 43.6 1.0 C A:ASP111 4.8 49.1 1.0 CB A:TYR115 4.8 42.0 1.0 CA A:ASP113 4.9 47.6 1.0 CG2 A:THR117 4.9 40.6 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