Sodium in PDB 5ay4: Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II)

The structure of Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II), PDB code: 5ay4 was solved by J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.000, 44.540, 27.550, 90.00, 109.10, 90.00
R / Rfree (%)	16 / 19.6

The structure of Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II) also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II) (pdb code 5ay4). 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 Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II), PDB code: 5ay4:

Sodium binding site 1 out of 1 in the Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rna Duplex Containing C-C Base Pairs Obtained in the Presence of Hg(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:22.4 occ:1.00 O3' B:C12 2.6 11.6 1.0 O2' B:C12 3.3 10.7 1.0 C3' B:C12 3.5 11.1 1.0 C4' B:C12 3.6 11.4 1.0 C2' B:C12 3.9 11.6 1.0 C5' B:C12 4.3 12.0 1.0 O4' B:C12 4.7 11.8 1.0 C1' B:C12 4.9 11.2 1.0

J.Kondo, Y.Tada, T.Dairaku, H.Saneyoshi, I.Okamoto, Y.Tanaka, A.Ono. High-Resolution Crystal Structure of A Silver(I)-Rna Hybrid Duplex Containing Watson-Crick-Like Csilver(I)C Metallo-Base Pairs Angew.Chem.Int.Ed.Engl. V. 54 13323 2015.
ISSN: ESSN 1521-3773
PubMed: 26448329
DOI: 10.1002/ANIE.201507894