Sodium 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:

Calcium

(Ca)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Dncs-1 Bound to the Ncs-1/RIC8A Protein/Protein Interaction Regulator Igs-1.76, PDB code: 6epa:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na206 b:53.1 occ:1.00 O A:ARG70 2.2 29.7 1.0 O A:HOH311 2.3 51.1 1.0 OD1 A:ASN76 2.3 60.8 1.0 O A:HOH405 2.3 56.0 1.0 O A:ASP73 2.4 34.3 1.0 HA A:GLU74 3.3 48.7 1.0 C A:ASP73 3.3 30.8 1.0 CG A:ASN76 3.4 49.0 1.0 C A:ARG70 3.4 25.1 1.0 HB3 A:ASP73 3.7 40.3 1.0 HA A:ARG70 3.8 37.7 1.0 HD21 A:ASN76 3.9 80.5 1.0 HA A:ASN76 3.9 53.0 1.0 CA A:GLU74 3.9 40.6 1.0 H A:ASN76 3.9 60.7 1.0 HB3 A:ARG70 4.0 47.6 1.0 HA A:VAL71 4.0 28.3 1.0 ND2 A:ASN76 4.0 67.1 1.0 N A:GLU74 4.0 29.6 1.0 CA A:ARG70 4.1 31.5 1.0 C A:GLU74 4.2 41.5 1.0 O A:GLU74 4.2 46.0 1.0 O A:HOH334 4.3 43.2 1.0 CA A:ASP73 4.3 25.3 1.0 H A:ASP73 4.4 28.5 1.0 CB A:ASP73 4.4 33.7 1.0 N A:ASN76 4.4 50.7 1.0 CA A:ASN76 4.4 44.2 1.0 N A:VAL71 4.4 24.1 1.0 CB A:ASN76 4.4 46.1 1.0 N A:ASP73 4.5 23.8 1.0 CA A:VAL71 4.6 23.6 1.0 CB A:ARG70 4.6 39.7 1.0 O A:VAL71 4.6 28.3 1.0 HH21 A:ARG106 4.7 72.3 1.0 C A:VAL71 4.7 27.6 1.0 CG A:ASP73 4.8 33.0 1.0 HB3 A:ASN76 4.8 55.3 1.0 HD22 A:ASN76 4.8 80.5 1.0 H A:GLU74 4.9 35.4 1.0 N A:ASN75 4.9 41.8 1.0 HD2 A:ARG70 5.0 78.3 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