Sodium in PDB 1jay: Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound

The structure of Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound, PDB code: 1jay was solved by E.Warkentin, B.Mamat, R.Thauer, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.900, 69.800, 145.500, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.6

The binding sites of Sodium atom in the Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound (pdb code 1jay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound, PDB code: 1jay:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:24.3 occ:1.00 O A:LEU174 2.4 20.7 1.0 O A:SER169 2.4 22.5 1.0 O A:ILE171 2.5 21.4 1.0 O A:HOH277 2.5 35.3 1.0 O A:HOH263 2.5 28.0 1.0 O A:HOH265 2.7 29.4 1.0 C A:SER169 3.4 22.7 1.0 C A:ILE171 3.4 21.9 1.0 C A:LEU174 3.6 20.0 1.0 N A:LEU174 3.8 19.1 1.0 CA A:SER169 3.9 22.4 1.0 CA A:ASP172 4.1 22.7 0.4 CA A:ASP172 4.1 23.9 0.6 N A:ASP172 4.1 21.8 0.4 N A:ASP172 4.1 22.4 0.6 N A:GLY173 4.1 22.3 1.0 N A:ILE171 4.1 21.6 1.0 CA A:LEU174 4.2 17.9 1.0 O A:ILE168 4.3 21.6 1.0 C A:GLU170 4.3 22.6 1.0 CA A:ILE171 4.4 20.9 1.0 OG A:SER169 4.4 29.3 1.0 O A:HOH275 4.4 30.8 1.0 C A:ASP172 4.5 23.4 0.6 C A:ASP172 4.5 22.5 0.4 N A:GLU170 4.5 22.3 1.0 CB A:LEU174 4.7 18.1 1.0 N A:ARG175 4.7 18.4 1.0 O A:GLU170 4.7 22.7 1.0 CB A:SER169 4.8 23.8 1.0 CA A:GLU170 4.8 23.4 1.0 C A:GLY173 4.8 19.0 1.0 OD2 A:ASP172 4.9 24.1 0.4 CA A:ARG175 5.0 17.6 1.0 N A:SER169 5.0 21.1 1.0

Sodium binding site 2 out of 2 in the Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) with Its Substrates Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1215 b:26.3 occ:1.00 O B:SER169 2.4 23.5 1.0 O B:LEU174 2.5 21.3 1.0 O B:ILE171 2.5 21.3 1.0 O B:HOH1263 2.6 27.6 1.0 O B:HOH1277 2.6 39.1 1.0 O B:HOH1265 2.8 41.7 1.0 C B:SER169 3.4 24.2 1.0 C B:ILE171 3.4 23.4 1.0 C B:LEU174 3.6 21.4 1.0 CA B:SER169 3.8 24.2 1.0 N B:LEU174 3.8 21.9 1.0 CA B:ASP172 4.1 26.9 1.0 N B:ASP172 4.1 24.3 1.0 N B:GLY173 4.1 25.0 1.0 N B:ILE171 4.2 21.9 1.0 CA B:LEU174 4.2 20.9 1.0 O B:ILE168 4.3 20.2 1.0 OG B:SER169 4.3 33.5 1.0 O B:HOH1275 4.4 28.7 1.0 CA B:ILE171 4.4 22.0 1.0 C B:GLU170 4.4 23.9 1.0 N B:GLU170 4.5 23.8 1.0 C B:ASP172 4.5 26.3 1.0 CB B:LEU174 4.6 19.4 1.0 N B:ARG175 4.7 19.2 1.0 O B:HOH1355 4.7 44.3 1.0 CB B:SER169 4.7 25.3 1.0 O B:GLU170 4.9 23.4 1.0 C B:GLY173 4.9 23.2 1.0 CA B:GLU170 4.9 23.3 1.0 N B:SER169 4.9 21.0 1.0

E.Warkentin, B.Mamat, M.Sordel-Klippert, M.Wicke, R.K.Thauer, M.Iwata, S.Iwata, U.Ermler, S.Shima. Structures of F420H2:Nadp+ Oxidoreductase with and Without Its Substrates Bound. Embo J. V. 20 6561 2001.
ISSN: ISSN 0261-4189
PubMed: 11726492
DOI: 10.1093/EMBOJ/20.23.6561