Sodium in PDB 2vkf: Complexes of Dodecin with Flavin and Flavin-Like Ligands

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2vkf was solved by M.Grininger, G.Noell, S.Trawoeger, E.Sinner, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.03 / 1.7
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	141.704, 141.704, 141.704, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.3

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Complexes of Dodecin with Flavin and Flavin-Like Ligands (pdb code 2vkf). 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 Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2vkf:

Sodium binding site 1 out of 1 in the Complexes of Dodecin with Flavin and Flavin-Like Ligands


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complexes of Dodecin with Flavin and Flavin-Like Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1063 b:15.1 occ:0.33 O A:HOH2079 2.3 11.0 1.0 O A:HOH2004 2.6 18.9 0.3 CL A:CL1064 2.7 13.2 0.3 O A:HOH2011 4.1 16.1 1.0 CB A:LEU7 4.4 9.4 1.0 NE2 A:GLN57 4.6 13.2 1.0 OE1 A:GLN57 4.7 11.7 1.0 O A:LYS5 4.7 9.8 1.0 CD2 A:LEU7 4.9 8.8 1.0 N A:LEU7 5.0 9.4 1.0

M.Grininger, G.Noell, S.Trawoeger, E.Sinner, D.Oesterhelt. Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified By Flavin-Dna Hybrid Linkers Biointerphases V. 3 51 2008.
ISSN: ISSN 1934-8630
PubMed: 20408700
DOI: 10.1116/1.2965134