Sodium in PDB 4etm: Crystal Structure of Yfkj From Bacillus Subtilis

All present enzymatic activity of Crystal Structure of Yfkj From Bacillus Subtilis:
3.1.3.48;

The structure of Crystal Structure of Yfkj From Bacillus Subtilis, PDB code: 4etm was solved by X.F.Cao, X.D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.37 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.152, 52.922, 86.609, 90.00, 102.84, 90.00
R / Rfree (%)	22.5 / 24.8

The structure of Crystal Structure of Yfkj From Bacillus Subtilis also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Yfkj From Bacillus Subtilis (pdb code 4etm). 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 Yfkj From Bacillus Subtilis, PDB code: 4etm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Yfkj From Bacillus Subtilis


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 Yfkj From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:21.9 occ:1.00 O A:HOH308 3.0 26.5 1.0 O A:PHE82 3.0 22.5 1.0 O A:LEU79 3.3 28.0 1.0 O A:ASP80 3.4 35.0 1.0 NE2 A:HIS107 3.7 17.6 1.0 CD2 A:HIS107 3.7 17.7 1.0 C A:ASP80 3.8 31.1 1.0 C A:PHE82 3.9 23.6 1.0 CA A:ASP80 4.0 29.1 1.0 O A:HOH444 4.2 41.9 1.0 C A:LEU79 4.3 23.1 1.0 CE1 A:HIS107 4.4 18.8 1.0 N A:PHE82 4.5 19.7 1.0 CA A:ASP83 4.5 20.0 1.0 CG A:HIS107 4.5 20.2 1.0 O A:HOH476 4.5 38.7 1.0 N A:ASP83 4.6 19.4 1.0 N A:ASP81 4.7 25.8 1.0 N A:ASP80 4.7 25.2 1.0 O A:HOH372 4.7 32.9 1.0 O A:HOH435 4.7 35.1 1.0 CA A:PHE82 4.8 21.9 1.0 O A:HOH347 4.8 37.9 1.0 C A:ASP81 4.8 24.9 1.0 O A:ASP83 4.9 22.0 1.0 ND1 A:HIS107 4.9 20.8 1.0 C A:ASP83 5.0 17.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Yfkj From Bacillus Subtilis


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 Yfkj From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:19.6 occ:1.00 O B:HOH365 2.9 45.6 1.0 O B:HOH340 3.0 31.4 1.0 O B:PHE82 3.0 19.2 1.0 O B:HOH319 3.1 25.6 1.0 O B:LEU79 3.2 23.8 1.0 O B:ASP80 3.2 24.0 1.0 O B:HOH338 3.4 34.3 1.0 NE2 B:HIS107 3.6 14.7 1.0 CD2 B:HIS107 3.7 17.1 1.0 C B:ASP80 3.7 22.0 1.0 C B:PHE82 3.9 14.5 1.0 O B:HOH511 4.0 44.7 1.0 CA B:ASP80 4.0 23.8 1.0 O B:HOH360 4.2 33.2 1.0 C B:LEU79 4.2 21.4 1.0 CE1 B:HIS107 4.4 16.0 1.0 N B:PHE82 4.5 19.1 1.0 CG B:HIS107 4.5 17.4 1.0 CA B:ASP83 4.5 19.1 1.0 O B:HOH544 4.6 37.3 1.0 O B:HOH403 4.6 28.2 1.0 N B:ASP80 4.6 19.3 1.0 N B:ASP83 4.6 16.5 1.0 N B:ASP81 4.7 17.5 1.0 C B:ASP81 4.8 20.9 1.0 CA B:PHE82 4.8 14.1 1.0 ND1 B:HIS107 4.9 18.0 1.0 O B:ASP83 4.9 18.4 1.0

X.F.Cao, X.D.Su. Crystal Structure of Yfkj From Bacillus Subtilis To Be Published.