Sodium in PDB 3tfh: Dmsp-Dependent Demethylase From P. Ubique - Apo

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

The structure of Dmsp-Dependent Demethylase From P. Ubique - Apo, PDB code: 3tfh 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)	43.51 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.656, 121.727, 59.648, 90.00, 101.01, 90.00
R / Rfree (%)	16.6 / 23.1

The binding sites of Sodium atom in the Dmsp-Dependent Demethylase From P. Ubique - Apo (pdb code 3tfh). 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 - Apo, PDB code: 3tfh:
Jump to Sodium binding site number: 1; 2;

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


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 - Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Na372 b:33.5 occ:1.00 O A:LEU36 2.7 27.5 1.0 OD2 A:ASP59 2.9 30.8 1.0 N A:ALA62 3.0 28.6 1.0 N A:ALA61 3.2 29.8 1.0 CB A:ALA62 3.5 27.5 1.0 CG A:ASP59 3.6 30.4 1.0 CA A:LEU37 3.6 28.1 1.0 CD1 A:LEU37 3.6 31.3 1.0 O A:ASP59 3.6 30.4 1.0 C A:VAL60 3.6 30.4 1.0 C A:LEU36 3.8 28.3 1.0 CG2 A:THR15 3.8 31.2 1.0 CA A:VAL60 3.8 32.3 1.0 CA A:ALA61 3.8 29.8 1.0 CA A:ALA62 3.8 28.7 1.0 C A:ALA61 3.9 29.3 1.0 O A:HOH441 3.9 32.8 1.0 CB A:LEU37 3.9 28.9 1.0 C A:ASP59 4.0 29.9 1.0 CB A:ALA61 4.0 29.6 1.0 OD1 A:ASP59 4.1 29.4 1.0 N A:LEU37 4.1 27.2 1.0 N A:VAL60 4.2 30.8 1.0 CD A:PRO38 4.2 27.2 1.0 O A:VAL60 4.4 31.1 1.0 CG A:LEU37 4.4 29.7 1.0 CB A:ASP59 4.6 28.4 1.0 CG A:MET35 4.8 28.3 1.0 SD A:MET35 4.8 29.9 1.0 C A:LEU37 4.9 26.7 1.0 CA A:ASP59 4.9 29.9 1.0 CB A:THR15 4.9 33.5 1.0 N A:PRO38 5.0 27.6 1.0

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


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 - Apo within 5.0Å range: probe atom residue distance (Å) B Occ B:Na370 b:34.4 occ:1.00 O B:LEU36 2.8 27.9 1.0 N B:ALA62 2.9 25.9 1.0 OD2 B:ASP59 2.9 26.5 1.0 N B:ALA61 3.2 26.3 1.0 CB B:ALA62 3.4 23.3 1.0 CD1 B:LEU37 3.7 27.9 1.0 C B:VAL60 3.7 28.5 1.0 CA B:LEU37 3.7 28.2 1.0 CA B:ALA62 3.7 25.1 1.0 C B:ALA61 3.8 26.8 1.0 CG B:ASP59 3.8 28.6 1.0 CA B:ALA61 3.8 26.8 1.0 C B:LEU36 3.8 26.8 1.0 CA B:VAL60 3.8 29.6 1.0 O B:ASP59 3.8 27.1 1.0 O B:HOH418 3.9 31.1 1.0 CB B:LEU37 3.9 27.7 1.0 CG2 B:THR15 4.0 26.2 1.0 CB B:ALA61 4.0 25.3 1.0 C B:ASP59 4.1 27.0 1.0 N B:LEU37 4.2 28.4 1.0 N B:VAL60 4.2 28.5 1.0 OD1 B:ASP59 4.3 26.1 1.0 CD B:PRO38 4.3 29.8 1.0 CG B:LEU37 4.5 28.0 1.0 O B:VAL60 4.6 27.2 1.0 CG B:MET35 4.7 25.5 1.0 SD B:MET35 4.7 26.4 1.0 CB B:ASP59 4.8 27.6 1.0 O B:ALA61 4.9 28.2 1.0 C B:LEU37 4.9 28.2 1.0 C B:ALA62 5.0 25.6 1.0 CB B:THR15 5.0 29.8 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