Sodium in PDB 3nd3: Uhelix 16-Mer Dsrna

The structure of Uhelix 16-Mer Dsrna, PDB code: 3nd3 was solved by B.H.Mooers, A.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.31 / 1.37
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	42.735, 42.735, 126.358, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.9

The structure of Uhelix 16-Mer Dsrna also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Uhelix 16-Mer Dsrna (pdb code 3nd3). 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 Uhelix 16-Mer Dsrna, PDB code: 3nd3:

Sodium binding site 1 out of 1 in the Uhelix 16-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Uhelix 16-Mer Dsrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na19 b:40.1 occ:1.00 O A:HOH419 2.3 33.2 1.0 O A:HOH319 2.3 51.0 1.0 O A:HOH119 2.3 45.2 1.0 O A:HOH219 2.3 39.1 1.0 O2' A:A5 2.5 35.6 1.0 O4' A:A6 2.6 37.0 1.0 HO2' A:A5 2.8 42.8 1.0 H4' A:A6 3.2 45.0 1.0 H5' A:A6 3.3 49.6 1.0 C4' A:A6 3.3 37.5 1.0 H1' A:A6 3.4 40.4 1.0 H2' A:A5 3.4 38.2 1.0 C2' A:A5 3.5 31.9 1.0 C1' A:A6 3.5 33.7 1.0 C5' A:A6 3.8 41.3 1.0 H1' A:A5 4.0 34.7 1.0 O A:HOH73 4.2 35.5 1.0 C1' A:A5 4.3 28.9 1.0 N9 A:A6 4.5 29.9 1.0 N3 A:A5 4.5 25.7 1.0 O2' A:A6 4.5 37.5 1.0 H5'' A:A6 4.5 49.6 1.0 C2' A:A6 4.6 36.1 1.0 O5' A:A6 4.6 37.5 1.0 H8 A:A6 4.6 39.2 1.0 C3' A:A6 4.6 39.3 1.0 C3' A:A5 4.7 33.3 1.0 O3' A:A5 4.8 35.2 1.0 C8 A:A6 4.9 32.7 1.0

B.H.Mooers, A.Singh. The Crystal Structure of An Oligo(U):Pre-Mrna Duplex From A Trypanosome Rna Editing Substrate. Rna V. 17 1870 2011.
ISSN: ISSN 1355-8382
PubMed: 21878548
DOI: 10.1261/RNA.2880311