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Sodium in PDB 2cc6: Complexes of Dodecin with Flavin and Flavin-Like Ligands

Protein crystallography data

The structure of Complexes of Dodecin with Flavin and Flavin-Like Ligands, PDB code: 2cc6 was solved by M.Grininger, K.Zeth, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.27
Space group F 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 141.720, 141.720, 141.720, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.2

Other elements in 2cc6:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Complexes of Dodecin with Flavin and Flavin-Like Ligands (pdb code 2cc6). 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: 2cc6:

Sodium binding site 1 out of 1 in 2cc6

Go back to Sodium Binding Sites List in 2cc6
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:Na104

b:11.9
occ:0.33
O A:HOH2072 2.3 11.6 1.0
O A:HOH2008 2.4 25.6 0.3
CL A:CL105 2.7 11.9 0.3
O A:HOH2010 4.2 12.8 1.0
CB A:LEU7 4.4 10.1 1.0
NE2 A:GLN59 4.6 11.1 1.0
OE1 A:GLN59 4.7 10.9 1.0
O A:LYS5 4.8 11.5 1.0
CD2 A:LEU7 4.8 9.7 1.0
N A:LEU7 5.0 10.1 1.0

Reference:

M.Grininger, K.Zeth, D.Oesterhelt. Dodecins: A Family of Lumichrome Binding Proteins. J.Mol.Biol. V. 357 842 2006.
ISSN: ISSN 0022-2836
PubMed: 16460756
DOI: 10.1016/J.JMB.2005.12.072
Page generated: Sun Aug 17 10:15:53 2025

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