Sodium in PDB 4b2h: Complexes of Dodecin with Flavin and Flavin-Like Ligands

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 4b2h was solved by Y.Yu, B.Heidel, T.L.Parapugna, S.Wenderhold-Reeb, B.Song, H.Schoenherr, M.Grininger, G.Noell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	142.005, 142.005, 142.005, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 17.8

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

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

The binding sites of Sodium atom in the Complexes of Dodecin with Flavin and Flavin-Like Ligands (pdb code 4b2h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 4b2h:
Jump to Sodium binding site number: 1; 2;

Sodium 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 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:Na101 b:35.0 occ:1.00 O A:HOH2072 2.0 46.4 1.0 O A:HOH2073 2.3 39.0 1.0 O A:HOH2074 2.4 33.5 1.0 O A:HOH2050 3.8 40.1 1.0 OE2 A:GLU38 4.1 24.0 1.0 OE1 A:GLU38 4.2 28.4 1.0 NZ A:LYS5 4.3 24.5 1.0 O4 A:C3F103 4.4 30.1 1.0 CD A:GLU38 4.6 28.8 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na104 b:14.7 occ:0.33 O A:HOH2008 2.3 14.9 1.0 CL A:CL106 2.7 14.9 0.3 O A:HOH2078 2.8 20.7 0.3 O A:HOH2007 4.2 17.6 1.0 CB A:LEU7 4.4 11.3 1.0 NE2 A:GLN57 4.6 13.8 1.0 OE1 A:GLN57 4.7 13.4 1.0 O A:LYS5 4.7 14.7 1.0 CD2 A:LEU7 4.8 12.6 1.0 N A:LEU7 5.0 11.8 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: ISSN 1433-7851
PubMed: 23532984
DOI: 10.1002/ANIE.201208987