Sodium in PDB 3i1j: Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae

The structure of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae, PDB code: 3i1j was solved by A.U.Singer, E.Evdokimova, M.Kudritska, A.M.Edwards, A.Joachimiak, A.Savchenko, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.46 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.253, 71.599, 131.086, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.4

The structure of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae (pdb code 3i1j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae, PDB code: 3i1j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na254 b:49.4 occ:1.00 OD1 A:ASP117 3.6 18.3 1.0 OE1 A:GLN120 3.9 31.9 1.0 CB A:ASP117 4.1 17.1 1.0 CA A:ASP117 4.1 18.2 1.0 CG A:ASP117 4.2 19.9 1.0 O A:ASP117 4.3 18.1 1.0 CA A:GLY105 4.4 18.7 1.0 CG2 A:VAL121 4.5 17.7 1.0 CD A:PRO106 4.5 19.7 1.0 CB A:GLN120 4.5 18.1 1.0 CD1 A:ILE103 4.6 20.7 1.0 CG A:GLN120 4.6 20.2 1.0 CD A:GLN120 4.7 30.0 1.0 C A:ASP117 4.7 17.7 1.0

Sodium binding site 2 out of 4 in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na250 b:41.7 occ:1.00 OD2 B:ASP115 3.0 30.9 1.0 O A:MSE131 3.1 15.9 1.0 OD1 B:ASP115 3.3 24.1 1.0 CG B:ASP115 3.6 24.9 1.0 C A:MSE131 3.7 17.9 1.0 CA A:MSE131 3.8 17.6 1.0 CB A:MSE131 3.8 18.7 1.0 CB A:TYR80 4.0 20.1 1.0 CB A:ALA135 4.2 16.8 1.0 N A:ALA135 4.2 17.7 1.0 CG A:MSE131 4.3 17.2 1.0 CB A:ALA77 4.3 22.9 1.0 NE A:ARG134 4.4 31.1 1.0 CA A:ALA77 4.4 22.3 1.0 CB A:ARG134 4.5 20.2 1.0 CA A:ALA135 4.6 17.6 1.0 CG A:TYR80 4.6 19.7 1.0 CD1 A:TYR80 4.6 20.3 1.0 NH1 A:ARG134 4.8 28.3 1.0 C A:ARG134 4.9 18.5 1.0 N A:LEU132 4.9 17.8 1.0 SE A:MSE131 5.0 24.1 1.0 CB B:ASP115 5.0 20.4 1.0

Sodium binding site 3 out of 4 in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na251 b:43.8 occ:1.00 O B:SER49 2.1 34.4 1.0 C B:SER49 3.2 34.4 1.0 N B:VAL53 3.2 25.1 1.0 O B:ALA22 3.2 28.8 1.0 CA B:LEU50 3.4 30.1 1.0 C B:LEU50 3.5 29.4 1.0 N B:GLU52 3.6 26.5 1.0 CG1 B:VAL53 3.6 23.2 1.0 N B:LEU50 3.7 32.2 1.0 CA B:ALA22 3.8 28.1 1.0 CB B:VAL53 3.8 24.4 1.0 CB B:GLU52 3.8 26.9 1.0 O B:LEU50 3.9 29.0 1.0 N B:ALA51 3.9 28.1 1.0 C B:ALA22 3.9 29.2 1.0 CA B:GLU52 4.0 26.6 1.0 C B:GLU52 4.1 25.4 1.0 CA B:VAL53 4.1 24.4 1.0 CB B:ALA22 4.2 28.3 1.0 O B:HOH299 4.4 41.3 1.0 C B:ALA51 4.5 26.9 1.0 CA B:SER49 4.5 35.9 1.0 CB B:LEU50 4.7 30.1 1.0 CA B:ALA51 4.8 27.2 1.0 CD2 B:LEU50 4.9 28.6 1.0 O B:ALA21 5.0 28.4 1.0

Sodium binding site 4 out of 4 in the Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na252 b:40.4 occ:1.00 OE2 B:GLU116 2.2 25.0 1.0 O2 A:EDO251 3.1 38.5 1.0 CD B:GLU116 3.2 20.1 1.0 O B:HOH297 3.4 35.5 1.0 CB A:ALA77 3.5 22.9 1.0 OE1 B:GLU116 3.6 18.7 1.0 O A:HOH265 3.7 15.2 1.0 C2 A:EDO251 3.9 37.2 1.0 OD2 B:ASP115 4.1 30.9 1.0 CG B:GLU116 4.4 21.1 1.0 CB B:ASP115 4.6 20.4 1.0 CA A:ALA77 4.7 22.3 1.0 CG B:ASP115 4.8 24.9 1.0 N A:ALA77 4.8 22.2 1.0 C1 A:EDO251 4.9 39.8 1.0

A.U.Singer, E.Evdokimova, M.Kudritska, A.M.Edwards, A.Savchenko. Structure of A Putative Short Chain Dehydrogenase From Pseudomonas Syringae To Be Published.