Sodium in PDB 2xdc: Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase.

The structure of Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase., PDB code: 2xdc was solved by N.Hoefer, D.Aragao, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.15 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.500, 62.560, 30.530, 90.00, 99.97, 90.00
R / Rfree (%)	17.9 / 21.4

The binding sites of Sodium atom in the Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase. (pdb code 2xdc). 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 Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase., PDB code: 2xdc:

Sodium binding site 1 out of 1 in the Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Linear Gramicidin D Obtained Using Type I Crystals Grown in A Lipid Cubic Phase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1018 b:48.7 occ:1.00 O6 A:15P1016 3.0 38.3 1.0 O1 A:15P1017 3.1 36.3 1.0 O7 A:15P1016 3.1 46.3 1.0 O5 A:15P1016 3.2 42.4 1.0 OXT A:15P1017 3.3 45.0 1.0 O2 A:15P1017 3.3 42.5 1.0 C11 A:15P1016 3.8 35.8 1.0 C13 A:15P1016 3.9 41.1 1.0 C12 A:15P1016 3.9 40.9 1.0 C1 A:15P1017 3.9 43.2 1.0 C4 A:15P1017 4.0 36.6 1.0 C14 A:15P1016 4.0 43.1 1.0 C2 A:15P1017 4.0 38.0 1.0 C3 A:15P1017 4.1 41.9 1.0 C10 A:15P1016 4.3 37.5 1.0 C9 A:15P1016 4.4 40.2 1.0 C5 A:15P1017 4.4 38.9 1.0 C6 A:15P1017 4.4 39.5 1.0

N.Hoefer, D.Aragao, M.Caffrey. Crystallizing Transmembrane Peptides in Lipidic Mesophases Biophys.J. V. 99 23 2010.
ISSN: ISSN 0006-3495
PubMed: 20682243
DOI: 10.1016/J.BPJ.2010.05.011