Sodium in PDB 6qi4: Ncs-1 Bound to A Ligand

The structure of Ncs-1 Bound to A Ligand, PDB code: 6qi4 was solved by M.J.Sanchez-Barrena, P.Blanco-Gabella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.35 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.729, 55.603, 77.725, 90.00, 94.97, 90.00
R / Rfree (%)	21.4 / 23.2

The structure of Ncs-1 Bound to A Ligand also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Ncs-1 Bound to A Ligand (pdb code 6qi4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ncs-1 Bound to A Ligand, PDB code: 6qi4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ncs-1 Bound to A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:21.6 occ:1.00 O B:PHE22 2.2 20.2 1.0 O B:THR20 2.3 24.6 1.0 O B:THR17 2.4 23.6 1.0 H B:PHE22 3.2 24.0 1.0 HG23 B:THR17 3.2 30.1 1.0 C B:PHE22 3.3 19.6 1.0 C B:THR20 3.3 28.3 1.0 N B:PHE22 3.4 20.0 1.0 HG22 B:THR17 3.4 30.1 1.0 C B:THR17 3.4 25.0 1.0 HA B:TYR21 3.5 27.8 1.0 HA B:THR17 3.6 31.0 1.0 CG2 B:THR17 3.7 25.1 1.0 H B:THR20 3.7 25.9 1.0 HG1 B:THR20 3.8 28.5 1.0 C B:TYR21 3.8 20.0 1.0 OG1 B:THR20 3.9 23.7 1.0 CA B:PHE22 3.9 20.6 1.0 CA B:TYR21 4.0 23.2 1.0 CA B:THR17 4.0 25.8 1.0 N B:TYR21 4.0 20.8 1.0 HA B:THR23 4.3 27.4 1.0 N B:THR23 4.3 22.1 1.0 CA B:THR20 4.4 17.8 1.0 N B:THR20 4.4 21.6 1.0 HA B:ARG18 4.4 32.6 1.0 HG21 B:THR17 4.5 30.1 1.0 CB B:THR17 4.5 22.7 1.0 N B:ARG18 4.5 24.9 1.0 HB2 B:PHE22 4.6 28.1 1.0 O B:TYR21 4.6 24.1 1.0 HA B:PHE22 4.6 24.7 1.0 O B:HOH396 4.7 32.1 1.0 CB B:THR20 4.8 26.8 1.0 CA B:THR23 4.8 22.8 1.0 H B:TYR21 4.8 25.0 1.0 CB B:PHE22 4.9 23.4 1.0 CA B:ARG18 4.9 27.2 1.0

Sodium binding site 2 out of 2 in the Ncs-1 Bound to A Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ncs-1 Bound to A Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Na205 b:40.2 occ:1.00 O C:THR17 2.2 44.3 1.0 O C:PHE22 2.4 38.9 1.0 O C:THR20 2.4 48.4 1.0 HG23 C:THR17 3.2 54.1 1.0 H C:PHE22 3.2 51.0 1.0 C C:THR17 3.3 46.6 1.0 C C:THR20 3.5 46.8 1.0 C C:PHE22 3.5 49.4 1.0 N C:PHE22 3.5 42.5 1.0 HG22 C:THR17 3.5 54.1 1.0 HA C:THR17 3.6 55.3 1.0 HA C:TYR21 3.6 42.3 1.0 H C:THR20 3.8 57.0 1.0 CG2 C:THR17 3.8 45.1 1.0 HG1 C:THR20 3.8 55.5 1.0 C C:TYR21 4.0 40.4 1.0 CA C:THR17 4.0 46.1 1.0 OG1 C:THR20 4.0 46.2 1.0 HA C:ARG18 4.1 51.8 1.0 CA C:TYR21 4.1 35.2 1.0 CA C:PHE22 4.2 39.7 1.0 N C:TYR21 4.2 34.7 1.0 HA C:THR23 4.3 66.8 1.0 N C:ARG18 4.4 50.5 1.0 N C:THR20 4.4 47.5 1.0 CA C:THR20 4.5 42.1 1.0 N C:THR23 4.5 46.1 1.0 CB C:THR17 4.5 49.5 1.0 O C:HOH354 4.5 46.2 1.0 HG21 C:THR17 4.5 54.1 1.0 CA C:ARG18 4.6 43.1 1.0 O C:TYR21 4.7 41.4 1.0 HB2 C:PHE22 4.7 49.6 1.0 HA C:PHE22 4.9 47.6 1.0 CA C:THR23 4.9 55.7 1.0 C C:ARG18 4.9 50.7 1.0 CB C:THR20 4.9 44.3 1.0

A.Canal-Martin, J.Sastre, M.J.Sanchez-Barrena, A.Canales, S.Baldominos, N.Pascual, L.Martinez-Gonzalez, D.Molero, M.E.Fernandez-Valle, E.Saez, P.Blanco-Gabella, E.Gomez-Rubio, S.Martin-Santamaria, A.Saiz, A.Mansilla, F.J.Canada, J.Jimenez-Barbero, A.Martinez, R.Perez-Fernandez. Insights Into Real-Time Chemical Processes in A Calcium Sensor Protein-Directed Dynamic Library. Nat Commun V. 10 2798 2019.
ISSN: ESSN 2041-1723
PubMed: 31243268
DOI: 10.1038/S41467-019-10627-W