Magnesium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2vkf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complexes of Dodecin with Flavin and Flavin-Like Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1061 b:33.3 occ:1.00 O A:HOH2053 2.2 25.8 1.0 O A:HOH2054 2.2 28.8 1.0 O A:HOH2086 4.0 53.0 0.5 OE2 A:GLU38 4.0 18.9 1.0 OE1 A:GLU38 4.1 22.6 1.0 NZ A:LYS5 4.2 20.8 1.0 O4 A:CF21066 4.4 20.3 1.0 CD A:GLU38 4.5 19.9 1.0

Magnesium binding site 2 out of 2 in the Complexes of Dodecin with Flavin and Flavin-Like Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complexes of Dodecin with Flavin and Flavin-Like Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1062 b:20.9 occ:1.00 OE2 A:GLU14 2.1 17.8 1.0 O A:HOH2023 2.1 19.4 1.0 O A:HOH2019 2.2 19.6 1.0 O A:HOH2022 2.2 19.4 1.0 CD A:GLU14 3.1 17.1 1.0 OE1 A:GLU14 3.4 17.1 1.0 O A:HOH2020 4.1 27.5 1.0 O A:GLU13 4.4 13.1 1.0 CG A:GLU14 4.4 15.5 1.0 CB A:GLU13 4.5 13.5 1.0 OE1 A:GLU13 4.6 25.4 1.0 C A:GLU13 4.9 12.8 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