Sodium in PDB 8hap: Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii

The structure of Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii, PDB code: 8hap was solved by S.Mine, M.Nakabayashi, K.Ishikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.075, 75.356, 105.305, 90, 124.64, 90
R / Rfree (%)	16.8 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii (pdb code 8hap). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii, PDB code: 8hap:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:34.1 occ:1.00 OD1 A:ASP245 2.9 38.6 1.0 N A:LEU398 3.2 27.2 1.0 N A:SER244 3.3 32.6 1.0 N A:ASP245 3.4 28.8 1.0 C A:SER244 3.4 28.4 1.0 CE2 A:PHE419 3.5 39.7 1.0 CA A:ASP245 3.6 28.7 1.0 CB A:TYR396 3.7 44.0 1.0 N A:GLY397 3.7 36.9 1.0 O A:SER244 3.7 29.6 1.0 CD2 A:PHE419 3.8 39.4 1.0 CA A:GLY243 3.9 35.1 1.0 CB A:LEU398 3.9 29.5 1.0 CA A:GLY397 3.9 35.4 1.0 CG A:ASP245 3.9 30.9 1.0 O A:GLN399 4.0 31.7 1.0 CA A:SER244 4.0 30.0 1.0 C A:GLY397 4.0 28.4 1.0 C A:TYR396 4.0 37.0 1.0 CA A:LEU398 4.0 26.9 1.0 C A:GLY243 4.1 33.2 1.0 N A:GLN399 4.1 28.9 1.0 CB A:ASP245 4.3 31.6 1.0 CA A:TYR396 4.4 38.5 1.0 CD A:PRO246 4.5 29.8 1.0 C A:LEU398 4.5 26.3 1.0 O A:TYR396 4.5 38.6 1.0 CZ A:PHE419 4.7 41.4 1.0 CG A:TYR396 4.8 44.2 1.0 CB A:SER244 4.8 30.4 1.0 C A:ASP245 4.9 29.0 1.0 OG1 A:THR443 4.9 49.6 1.0 CG2 A:THR394 4.9 49.2 1.0 C A:GLN399 5.0 30.3 1.0 O A:HOH655 5.0 41.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From Hyperthermophilic Archaeon Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:35.7 occ:1.00 OD1 B:ASP245 2.9 35.7 1.0 N B:SER244 3.2 33.8 1.0 N B:LEU398 3.2 29.1 1.0 N B:ASP245 3.5 33.3 1.0 C B:SER244 3.5 32.5 1.0 CE2 B:PHE419 3.6 40.6 1.0 CA B:ASP245 3.6 31.3 1.0 O B:SER244 3.7 34.9 1.0 N B:GLY397 3.8 42.4 1.0 CB B:TYR396 3.8 46.8 1.0 CB B:LEU398 3.8 32.1 1.0 CA B:GLY243 3.9 35.4 1.0 CD2 B:PHE419 3.9 37.7 1.0 O B:GLN399 4.0 35.4 1.0 CA B:SER244 4.0 32.0 1.0 C B:GLY243 4.0 29.6 1.0 CG B:ASP245 4.0 33.6 1.0 CA B:GLY397 4.0 36.1 1.0 CA B:LEU398 4.1 30.4 1.0 C B:GLY397 4.1 33.2 1.0 C B:TYR396 4.1 44.1 1.0 N B:GLN399 4.1 31.9 1.0 CB B:ASP245 4.4 33.4 1.0 CD B:PRO246 4.5 29.9 1.0 C B:LEU398 4.5 28.2 1.0 O B:TYR396 4.6 53.2 1.0 CA B:TYR396 4.6 44.4 1.0 CZ B:PHE419 4.8 43.0 1.0 CB B:SER244 4.8 34.0 1.0 OG1 B:THR443 4.8 48.4 1.0 C B:ASP245 4.9 31.3 1.0 C B:GLN399 4.9 34.9 1.0 CG B:TYR396 5.0 47.0 1.0

S.Mine, M.Nakabayashi, K.Ishikawa. Crystal Structure of Thermostable Acetaldehyde Dehydrogenase From the Hyperthermophilic Archaeon Sulfolobus Tokodaii. Acta Crystallogr.,Sect.F V. 79 159 2023.
ISSN: ESSN 2053-230X
PubMed: 37227376
DOI: 10.1107/S2053230X23004430