Magnesium in PDB 4b2m: Complexes of Dodecin with Flavin and Flavin-Like Ligands

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 4b2m was solved by H.Staudt, M.Hoesl, A.Dreuw, S.Serdjukow, D.Oesterhelt, N.Budisa, J.Wachtveitl, M.Grininger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	142.574, 142.574, 142.574, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.5

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 4b2m). 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: 4b2m:
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:Mg101 b:36.5 occ:1.00 O A:HOH2028 2.1 22.6 1.0 O A:HOH2029 2.1 20.9 1.0 OE2 A:GLU14 2.2 25.4 1.0 O A:HOH2023 2.2 35.8 1.0 O A:HOH2024 2.3 29.4 1.0 CD A:GLU14 3.1 23.6 1.0 OE1 A:GLU14 3.4 23.5 1.0 OE1 A:GLU51 3.7 0.4 1.0 OE2 A:GLU51 4.5 65.9 1.0 CD A:GLU51 4.6 88.5 1.0 CG A:GLU14 4.6 20.4 1.0 O A:GLU13 4.6 18.2 1.0 CB A:GLU13 4.6 22.7 1.0 OE1 A:GLU13 4.6 40.7 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:Mg102 b:72.3 occ:1.00 O A:HOH2065 2.4 50.5 1.0 O A:HOH2064 3.4 46.8 1.0 O4 A:RBF1067 3.9 37.5 1.0 OE2 A:GLU38 4.0 33.0 1.0 NZ A:LYS5 4.1 25.7 1.0 OE1 A:GLU38 4.6 46.0 1.0 CD A:GLU38 4.8 40.7 1.0

Y.Yu, B.Heidel, T.L.Parapugna, S.Wenderhold-Reeb, B.Song, H.Schonherr, M.Grininger, G.Noll. The Flavoprotein Dodecin As A Redox Probe For Electron Transfer Through Dna. Angew.Chem.Int.Ed.Engl. V. 52 4950 2013.
ISSN: ESSN 1521-3773
PubMed: 23532984
DOI: 10.1002/ANIE.201208987