Sodium in PDB 1jax: Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno)

The structure of Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno), PDB code: 1jax 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)	19.86 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.640, 72.140, 70.400, 90.00, 90.12, 90.00
R / Rfree (%)	18.5 / 22.1

The structure of Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Structure of Coenzyme F420H2:Nadp+ Oxidoreductase (Fno) (pdb code 1jax). 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), PDB code: 1jax:
Jump to Sodium binding site number: 1; 2;

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:21.1 occ:1.00 O A:HOH257 2.3 41.5 1.0 O A:SER169 2.4 13.1 0.5 O A:LEU174 2.4 11.9 1.0 O A:SER169 2.6 13.9 0.5 O A:HOH249 2.6 27.7 1.0 O A:HOH248 2.7 23.6 1.0 O A:ILE171 2.8 12.6 1.0 C A:SER169 3.4 14.8 0.5 C A:SER169 3.4 15.3 0.5 C A:ILE171 3.5 13.9 1.0 C A:LEU174 3.6 13.1 1.0 CA A:SER169 3.9 14.1 0.5 CA A:SER169 3.9 14.8 0.5 N A:LEU174 4.0 14.3 1.0 O A:ILE168 4.1 13.9 1.0 CA A:ASP172 4.1 12.4 0.5 N A:ASP172 4.1 12.9 0.5 N A:ILE171 4.1 12.4 1.0 N A:ASP172 4.1 14.7 0.5 CA A:ASP172 4.1 15.6 0.5 N A:GLY173 4.3 14.0 1.0 O A:HOH255 4.3 26.5 1.0 CA A:LEU174 4.3 13.0 1.0 N A:GLU170 4.4 12.6 1.0 C A:GLU170 4.4 14.1 1.0 CA A:ILE171 4.4 13.3 1.0 OG A:SER169 4.5 18.0 0.5 C A:ASP172 4.6 13.3 0.5 C A:ASP172 4.6 15.4 0.5 N A:ARG175 4.7 11.9 1.0 O A:HOH344 4.7 34.0 1.0 OD2 A:ASP172 4.7 11.6 0.5 CB A:LEU174 4.8 11.3 1.0 CB A:SER169 4.8 16.5 0.5 CA A:GLU170 4.8 14.7 1.0 CB A:SER169 4.9 17.4 0.5 CA A:ARG175 4.9 13.0 1.0 N A:SER169 4.9 14.4 0.5 N A:SER169 4.9 14.7 0.5 C A:ILE168 4.9 13.9 1.0 O A:GLU170 4.9 13.1 1.0

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na215 b:30.7 occ:1.00 O B:SER169 2.5 14.9 0.5 O B:SER169 2.5 14.8 0.5 O B:LEU174 2.6 14.2 1.0 O B:HOH1263 2.8 21.2 1.0 O B:HOH1277 3.0 43.0 1.0 O B:ILE171 3.0 14.1 1.0 O B:HOH1265 3.2 37.4 1.0 C B:SER169 3.3 15.2 0.5 C B:SER169 3.3 15.2 0.5 CA B:SER169 3.6 14.5 0.5 CA B:SER169 3.6 14.6 0.5 C B:LEU174 3.7 13.6 1.0 C B:ILE171 3.9 16.8 1.0 N B:LEU174 4.0 13.8 1.0 O B:ILE168 4.3 13.9 1.0 CB B:SER169 4.3 15.6 0.5 N B:GLY173 4.4 18.8 1.0 CB B:SER169 4.4 15.8 0.5 CA B:LEU174 4.4 12.9 1.0 N B:GLU170 4.5 14.4 1.0 CA B:ASP172 4.5 20.8 1.0 N B:ILE171 4.5 14.5 1.0 O B:HOH1275 4.5 30.2 1.0 N B:ASP172 4.5 17.2 1.0 C B:GLU170 4.7 17.0 1.0 N B:ARG175 4.8 12.9 1.0 N B:SER169 4.8 14.3 0.5 N B:SER169 4.8 14.3 0.5 C B:ASP172 4.8 19.6 1.0 CA B:ILE171 4.9 15.3 1.0 CB B:LEU174 4.9 12.2 1.0 CA B:ARG175 4.9 12.5 1.0 CA B:GLU170 5.0 16.3 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