Sodium in PDB 3tfi: Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp

All present enzymatic activity of Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp:
2.1.2.10;

The structure of Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp, PDB code: 3tfi was solved by D.J.Schuller, C.R.Reisch, M.A.Moran, W.B.Whitman, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.20 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.752, 121.992, 59.373, 90.00, 100.17, 90.00
R / Rfree (%)	13 / 18.4

The binding sites of Sodium atom in the Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp (pdb code 3tfi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp, PDB code: 3tfi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na372 b:20.3 occ:1.00 O A:LEU36 2.9 13.4 1.0 OD2 A:ASP59 2.9 15.6 1.0 N A:ALA62 2.9 13.5 1.0 N A:ALA61 3.1 13.9 1.0 CB A:ALA62 3.4 14.0 1.0 O A:ASP59 3.6 16.1 1.0 CD1 A:LEU37 3.6 17.2 1.0 C A:VAL60 3.6 14.5 1.0 CA A:LEU37 3.7 11.1 1.0 CG A:ASP59 3.7 15.8 1.0 CA A:ALA62 3.8 13.9 1.0 CA A:VAL60 3.8 15.4 1.0 CA A:ALA61 3.8 15.0 1.0 C A:ALA61 3.8 13.7 1.0 CG2 A:THR15 3.8 15.8 1.0 C A:LEU36 3.9 11.9 1.0 C A:ASP59 4.0 14.0 1.0 O A:HOH418 4.0 19.6 1.0 CB A:ALA61 4.1 14.9 1.0 CB A:LEU37 4.1 13.2 1.0 N A:VAL60 4.1 14.6 1.0 OD1 A:ASP59 4.1 16.0 1.0 N A:LEU37 4.2 11.6 1.0 CD A:PRO38 4.3 13.7 1.0 O A:VAL60 4.5 14.9 1.0 CG A:LEU37 4.5 14.4 1.0 CG A:MET35 4.6 14.5 1.0 CB A:ASP59 4.7 14.7 1.0 SD A:MET35 4.8 16.0 1.0 C A:LEU37 4.9 11.2 1.0 CA A:ASP59 4.9 14.0 1.0 CB A:THR15 5.0 16.4 1.0 O A:ALA61 5.0 15.4 1.0 N A:PRO38 5.0 11.2 1.0

Sodium binding site 2 out of 2 in the Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dmsp-Dependent Demethylase From P. Ubique - with Substrate Dmsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na372 b:20.3 occ:1.00 O B:LEU36 2.8 12.6 1.0 N B:ALA62 2.9 11.1 1.0 OD2 B:ASP59 2.9 14.2 1.0 N B:ALA61 3.2 13.0 1.0 CB B:ALA62 3.4 13.3 1.0 CD1 B:LEU37 3.6 15.4 1.0 O B:ASP59 3.6 14.7 1.0 C B:VAL60 3.7 11.4 1.0 CA B:LEU37 3.7 10.8 1.0 CG B:ASP59 3.7 13.9 1.0 CA B:ALA62 3.8 11.1 1.0 CA B:ALA61 3.8 11.8 1.0 C B:ALA61 3.8 11.9 1.0 CA B:VAL60 3.8 12.3 1.0 C B:LEU36 3.8 11.9 1.0 O B:HOH439 3.9 16.9 1.0 CG2 B:THR15 3.9 14.3 1.0 CB B:ALA61 4.0 14.5 1.0 C B:ASP59 4.0 13.1 1.0 CB B:LEU37 4.1 11.9 1.0 N B:VAL60 4.2 13.0 1.0 OD1 B:ASP59 4.2 14.5 1.0 N B:LEU37 4.2 11.8 1.0 CD B:PRO38 4.2 13.3 1.0 CG B:LEU37 4.5 11.8 1.0 O B:VAL60 4.5 13.1 1.0 CG B:MET35 4.7 12.6 1.0 CB B:ASP59 4.7 13.2 1.0 SD B:MET35 4.8 13.0 1.0 C B:LEU37 4.9 11.1 1.0 O B:ALA61 5.0 12.0 1.0 N B:PRO38 5.0 12.1 1.0 CB B:THR15 5.0 14.3 1.0 CA B:ASP59 5.0 12.8 1.0

D.J.Schuller, C.R.Reisch, M.A.Moran, W.B.Whitman, W.N.Lanzilotta. Structures of Dimethylsulfoniopropionate-Dependent Demethylase From the Marine Organism Pelagabacter Ubique. Protein Sci. V. 21 289 2012.
ISSN: ISSN 0961-8368
PubMed: 22162093
DOI: 10.1002/PRO.2015