Calcium in PDB 6epa: Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76

The structure of Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76, PDB code: 6epa was solved by M.J.Sanchez-Barrena, M.Daniel, L.Infantes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.11 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.843, 55.456, 61.259, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.2

The structure of Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76 (pdb code 6epa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76, PDB code: 6epa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:31.1 occ:1.00 O A:ALA79 2.2 26.6 1.0 O A:HOH331 2.3 41.6 1.0 OD1 A:ASP77 2.3 49.4 1.0 OD1 A:ASP73 2.3 30.6 1.0 OD1 A:ASN75 2.4 44.6 1.0 OE1 A:GLU84 2.4 26.5 1.0 OE2 A:GLU84 2.5 32.9 1.0 CD A:GLU84 2.8 32.5 1.0 CG A:ASP77 3.1 43.5 1.0 HD21 A:ASN75 3.1 60.2 1.0 CG A:ASN75 3.2 46.3 1.0 OD2 A:ASP77 3.4 54.5 1.0 H A:ASP77 3.4 47.0 1.0 CG A:ASP73 3.5 33.0 1.0 ND2 A:ASN75 3.5 50.2 1.0 C A:ALA79 3.5 21.8 1.0 H A:ALA79 3.5 39.4 1.0 HA A:ASP73 3.5 30.3 1.0 HA A:ILE80 3.7 32.6 1.0 H A:ASN75 3.8 50.1 1.0 H A:GLU81 3.8 33.1 1.0 H A:ASN76 4.1 60.7 1.0 HG2 A:GLU81 4.2 46.5 1.0 N A:ALA79 4.2 32.9 1.0 N A:ASP77 4.2 39.2 1.0 CA A:ASP73 4.2 25.3 1.0 HD22 A:ASN75 4.3 60.2 1.0 OD2 A:ASP73 4.3 32.6 1.0 CB A:ASP73 4.3 33.7 1.0 CG A:GLU84 4.3 29.5 1.0 CB A:ASP77 4.3 44.4 1.0 N A:ILE80 4.4 25.7 1.0 CA A:ALA79 4.4 29.2 1.0 HB3 A:ALA79 4.5 51.4 1.0 CA A:ILE80 4.5 27.2 1.0 HB2 A:ASP73 4.5 40.3 1.0 CB A:ASN75 4.5 41.6 1.0 C A:ASP73 4.5 30.8 1.0 HB3 A:ASP77 4.5 53.2 1.0 N A:ASN75 4.5 41.8 1.0 N A:GLU81 4.5 27.7 1.0 H A:GLY78 4.6 41.5 1.0 N A:ASN76 4.6 50.7 1.0 H A:GLU74 4.6 35.4 1.0 HG3 A:GLU84 4.6 35.4 1.0 CA A:ASP77 4.7 40.1 1.0 HG2 A:GLU84 4.7 35.4 1.0 N A:GLU74 4.8 29.6 1.0 HB3 A:ASN75 4.8 49.9 1.0 CD A:GLU81 4.8 64.5 1.0 N A:GLY78 4.8 34.7 1.0 HB2 A:GLU84 4.9 30.6 1.0 CA A:ASN75 4.9 47.3 1.0 OE1 A:GLU81 4.9 50.3 1.0 CG A:GLU81 4.9 38.8 1.0 HB3 A:GLU81 4.9 34.5 1.0 C A:ASN75 4.9 55.4 1.0 C A:ASP77 4.9 38.4 1.0 O A:ASP73 5.0 34.3 1.0 CB A:ALA79 5.0 42.8 1.0 C A:ILE80 5.0 24.5 1.0

Calcium binding site 2 out of 3 in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:31.7 occ:1.00 O A:ARG162 2.3 28.1 1.0 OD1 A:ASP156 2.4 34.0 1.0 OD1 A:ASN158 2.4 39.8 1.0 OE1 A:GLU167 2.4 26.5 1.0 OD1 A:ASP160 2.4 39.7 1.0 OE2 A:GLU167 2.5 33.1 1.0 O A:HOH304 2.5 30.2 1.0 CD A:GLU167 2.8 33.2 1.0 CG A:ASP160 3.2 47.8 1.0 CG A:ASN158 3.4 35.0 1.0 CG A:ASP156 3.5 32.3 1.0 OD2 A:ASP160 3.5 44.5 1.0 C A:ARG162 3.5 31.6 1.0 H A:ASP160 3.5 44.3 1.0 HA A:LEU163 3.6 30.2 1.0 HA A:ASP156 3.6 39.9 1.0 H A:ARG162 3.6 36.5 1.0 HD21 A:ASN158 3.6 43.3 1.0 H A:ASN158 3.7 55.6 1.0 ND2 A:ASN158 3.9 36.1 1.0 HD23 A:LEU163 4.0 36.0 1.0 H A:THR164 4.0 34.4 1.0 HG3 A:ARG162 4.1 53.4 1.0 HG23 A:THR164 4.2 32.9 1.0 OD2 A:ASP156 4.2 34.7 1.0 CG A:GLU167 4.3 37.0 1.0 CA A:ASP156 4.3 33.3 1.0 CA A:LEU163 4.3 25.2 1.0 N A:ARG162 4.3 30.5 1.0 N A:LEU163 4.4 28.5 1.0 N A:ASP160 4.4 37.0 1.0 HG2 A:ARG162 4.4 53.4 1.0 CB A:ASP156 4.4 36.9 1.0 H A:HIS159 4.4 46.4 1.0 H A:LYS157 4.4 44.3 1.0 N A:ASN158 4.5 46.4 1.0 CB A:ASP160 4.5 40.8 1.0 CA A:ARG162 4.5 38.1 1.0 C A:ASP156 4.6 42.5 1.0 HG3 A:GLU167 4.6 44.3 1.0 CG A:ARG162 4.6 44.5 1.0 O A:HOH359 4.7 45.0 1.0 HB2 A:ASP156 4.7 44.2 1.0 N A:LYS157 4.7 37.0 1.0 CB A:ASN158 4.7 47.3 1.0 N A:HIS159 4.7 38.7 1.0 HG2 A:GLU167 4.7 44.3 1.0 N A:THR164 4.7 28.7 1.0 HB3 A:ASP160 4.7 48.9 1.0 HD22 A:ASN158 4.8 43.3 1.0 C A:ASN158 4.9 41.4 1.0 H A:ASP161 4.9 45.2 1.0 CA A:ASP160 4.9 29.7 1.0 CA A:ASN158 4.9 41.0 1.0 CD2 A:LEU163 4.9 30.0 1.0 HB2 A:GLU167 4.9 34.8 1.0 HD22 A:LEU163 4.9 36.0 1.0 C A:LEU163 5.0 24.4 1.0

Calcium binding site 3 out of 3 in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:26.3 occ:1.00 O A:TYR115 2.3 26.2 1.0 OD1 A:ASP111 2.3 40.7 1.0 O A:HOH351 2.3 33.7 1.0 OD1 A:ASP113 2.4 29.3 1.0 OD1 A:ASP109 2.4 26.6 1.0 OE2 A:GLU120 2.4 32.4 1.0 OE1 A:GLU120 2.4 28.1 1.0 CD A:GLU120 2.8 29.7 1.0 CG A:ASP113 3.2 30.9 1.0 CG A:ASP111 3.3 43.5 1.0 H A:ASP113 3.3 32.8 1.0 HA A:ASP109 3.4 25.4 1.0 CG A:ASP109 3.4 34.2 1.0 C A:TYR115 3.5 23.5 1.0 H A:TYR115 3.5 27.2 1.0 H A:ASP111 3.5 37.1 1.0 OD2 A:ASP113 3.7 35.5 1.0 HA A:ILE116 3.8 29.0 1.0 OD2 A:ASP111 3.8 37.3 1.0 HG23 A:THR117 3.9 48.7 1.0 HB2 A:TYR115 4.1 29.2 1.0 CA A:ASP109 4.1 21.2 1.0 H A:ASN112 4.2 34.5 0.5 H A:ASN112 4.2 34.5 0.5 N A:ASP113 4.2 27.4 1.0 N A:TYR115 4.2 22.8 1.0 H A:THR117 4.2 39.5 1.0 OD2 A:ASP109 4.3 26.1 1.0 CB A:ASP109 4.3 23.9 1.0 N A:ASP111 4.3 31.0 1.0 CG A:GLU120 4.3 30.1 1.0 C A:ASP109 4.3 27.2 1.0 H A:VAL110 4.3 38.4 1.0 CB A:ASP113 4.3 27.4 1.0 HB3 A:ASP113 4.3 32.8 1.0 CA A:TYR115 4.3 23.2 1.0 N A:ILE116 4.4 27.8 1.0 N A:VAL110 4.5 32.1 1.0 HB2 A:ASP109 4.5 28.6 1.0 CA A:ILE116 4.5 24.2 1.0 N A:ASN112 4.5 28.8 1.0 CB A:ASP111 4.5 29.3 1.0 HG3 A:GLU120 4.6 36.0 1.0 H A:GLY114 4.7 33.0 1.0 CB A:TYR115 4.7 24.4 1.0 HG2 A:GLU120 4.7 36.0 1.0 CA A:ASP113 4.7 27.2 1.0 CA A:ASP111 4.7 31.3 1.0 C A:ASP111 4.7 30.2 1.0 N A:THR117 4.8 32.9 1.0 O A:ASP109 4.8 30.2 1.0 CG2 A:THR117 4.8 40.6 1.0 HB3 A:ASP111 4.9 35.1 1.0 N A:GLY114 5.0 27.5 1.0

C.Roca, L.Martinez-Gonzalez, M.Daniel-Mozo, J.Sastre, L.Infantes, A.Mansilla, A.Chaves-Sanjuan, J.M.Gonzalez-Rubio, C.Gil, F.J.Canada, A.Martinez, M.J.Sanchez-Barrena, N.E.Campillo. Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor RIC8A with A Small Phenothiazine Molecule For the Rational Generation of Therapeutic Synapse Function Regulators. J. Med. Chem. V. 61 5910 2018.
ISSN: ISSN 1520-4804
PubMed: 29966094
DOI: 10.1021/ACS.JMEDCHEM.8B00088