Sodium in PDB 2vyx: Crystal Structure of the T. Thermophilus Dodecin W38F Mutant

The structure of Crystal Structure of the T. Thermophilus Dodecin W38F Mutant, PDB code: 2vyx was solved by L.-O.Essen, B.Meissner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.630, 98.550, 139.840, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25

The structure of Crystal Structure of the T. Thermophilus Dodecin W38F Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the T. Thermophilus Dodecin W38F Mutant (pdb code 2vyx). 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 the T. Thermophilus Dodecin W38F Mutant, PDB code: 2vyx:

Sodium binding site 1 out of 1 in the Crystal Structure of the T. Thermophilus Dodecin W38F Mutant


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 the T. Thermophilus Dodecin W38F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1073 b:33.4 occ:1.00 O D:HOH2039 2.5 22.1 1.0 O D:HOH2031 2.8 25.5 1.0 O F:HOH2044 3.0 20.1 1.0 OE1 D:GLU55 3.9 21.5 1.0 O2 F:FMN1070 3.9 14.3 1.0 NZ I:LYS3 4.0 34.5 1.0 C4' F:FMN1072 4.0 20.7 1.0 C5' F:FMN1072 4.0 23.2 1.0 CG2 D:THR47 4.2 16.6 1.0 O F:HOH2050 4.2 52.7 1.0 O F:HOH2043 4.2 26.8 1.0 NE2 D:GLN57 4.3 17.4 1.0 O4' F:FMN1072 4.3 23.0 1.0 O D:HOH2013 4.3 42.8 1.0 O D:HOH2038 4.4 40.0 1.0 CD D:GLU55 4.4 24.4 1.0 OE2 D:GLU55 4.4 27.0 1.0 CE I:LYS3 4.8 33.1 1.0 OG1 D:THR47 4.8 18.1 1.0 CB D:THR47 5.0 16.2 1.0

G.G.Gurzadyan, B.Meissner, B.Sander, L.-O.Essen, M.E.Michel-Beyerle. Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin To Be Published.