Sodium in PDB 2dv3: Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase

All present enzymatic activity of Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase:
2.1.1.98;

The structure of Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase, PDB code: 2dv3 was solved by H.Mizutani, Y.Matsuura, N.Kunishima, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.197, 104.197, 137.827, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 23.4

The structure of Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase (pdb code 2dv3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase, PDB code: 2dv3:

Sodium binding site 1 out of 1 in the Crystal Structure of LEU65 to Arg Mutant of Diphthine Synthase


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 LEU65 to Arg Mutant of Diphthine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:28.0 occ:1.00 O A:HOH1374 2.1 25.8 1.0 O B:HOH1507 2.2 24.7 1.0 OH A:TYR117 2.4 27.3 1.0 O B:HOH1516 2.5 27.0 1.0 O B:HOH1503 2.6 25.3 1.0 CZ A:TYR117 3.3 27.2 1.0 CE2 A:TYR117 3.7 27.0 1.0 O B:GLY131 3.9 21.9 1.0 OG B:SER133 4.0 26.2 1.0 O A:PHE130 4.1 26.7 1.0 CD1 B:TYR117 4.2 22.4 1.0 CE1 B:TYR117 4.3 22.4 1.0 O A:ILE127 4.3 22.0 1.0 O A:HOH1305 4.3 22.6 1.0 CB A:PHE130 4.4 23.7 1.0 O B:HOH1504 4.4 25.0 1.0 CB B:PHE130 4.4 24.7 1.0 CE1 A:TYR117 4.4 26.0 1.0 O A:HOH1307 4.5 25.7 1.0 O B:HOH1505 4.7 23.3 1.0 C A:PHE130 4.8 26.6 1.0 O B:PHE130 4.8 22.8 1.0 O A:GLY131 4.9 23.9 1.0

H.Mizutani, Y.Matsuura, N.Kunishima. Crystal Structure of Diphthine Synthase From Pyrococcus Horikoshii OT3 To Be Published.