Sodium in PDB 8gn9: Spfh Domain of Pyrococcus Horikoshii Stomatin

The structure of Spfh Domain of Pyrococcus Horikoshii Stomatin, PDB code: 8gn9 was solved by T.Komatsu, I.Matsui, H.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	28.014, 28.014, 240.63, 90, 90, 90
R / Rfree (%)	21.5 / 27.8

The binding sites of Sodium atom in the Spfh Domain of Pyrococcus Horikoshii Stomatin (pdb code 8gn9). 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 Spfh Domain of Pyrococcus Horikoshii Stomatin, PDB code: 8gn9:

Sodium binding site 1 out of 1 in the Spfh Domain of Pyrococcus Horikoshii Stomatin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Spfh Domain of Pyrococcus Horikoshii Stomatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:34.4 occ:1.00 OD1 A:ASP152 2.0 37.1 1.0 O A:ASP148 2.1 29.3 1.0 OG1 A:THR151 2.3 27.4 1.0 OD1 A:ASP148 2.4 29.1 1.0 O A:ILE156 2.4 28.8 1.0 C A:ASP148 3.0 32.4 1.0 CG A:ASP152 3.1 36.8 1.0 N A:ASP152 3.1 35.4 1.0 CG A:ASP148 3.3 34.8 1.0 CA A:ASP148 3.3 33.6 1.0 CB A:THR151 3.4 32.5 1.0 C A:THR151 3.5 35.6 1.0 C A:ILE156 3.5 33.3 1.0 CA A:ASP152 3.6 34.9 1.0 CA A:THR151 3.7 34.0 1.0 CB A:ASP152 3.8 34.6 1.0 CA A:LYS157 3.8 39.2 1.0 N A:THR151 3.9 34.4 1.0 CB A:ASP148 3.9 34.6 1.0 N A:VAL158 4.0 38.7 1.0 OD2 A:ASP152 4.1 39.1 1.0 N A:LYS157 4.1 36.0 1.0 OD2 A:ASP148 4.1 38.9 1.0 O A:THR151 4.2 39.0 1.0 N A:GLU149 4.2 33.6 1.0 O A:ILE147 4.3 33.0 1.0 C A:LYS157 4.4 37.9 1.0 CE A:LYS157 4.5 53.5 1.0 N A:ASP148 4.5 31.8 1.0 CG2 A:VAL158 4.5 36.0 1.0 CD A:LYS157 4.6 52.5 1.0 CG2 A:THR151 4.7 34.4 1.0 NZ A:LYS157 4.7 51.3 1.0 CA A:ILE156 4.8 33.8 1.0 C A:GLU149 4.8 33.8 1.0 C A:ILE147 4.8 33.8 1.0 CA A:GLU149 4.9 36.0 1.0 O A:GLU149 5.0 31.6 1.0 CB A:LYS157 5.0 44.0 1.0 CG A:LYS157 5.0 49.7 1.0 CB A:VAL158 5.0 39.7 1.0

T.Komatsu, I.Matsui, H.Yokoyama. Structural and Mutational Studies Suggest Key Residues to Determine Whether Stomatin Spfh Domains Form Dimers or Trimers. Biochem Biophys Rep V. 32 01384 2022.
ISSN: ESSN 2405-5808
PubMed: 36386441
DOI: 10.1016/J.BBREP.2022.101384