Sodium in PDB 8ami: Crystal Structure of Auguggcau Duplex with Barium Ions (Model 2)

The structure of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 2), PDB code: 8ami was solved by A.Kiliszek, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.46 / 1.79
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	34.109, 34.109, 81.353, 90, 90, 90
R / Rfree (%)	18.3 / 23.6

The structure of Crystal Structure of Auguggcau Duplex with Barium Ions (Model 2) also contains other interesting chemical elements:

Barium

(Ba)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 2) (pdb code 8ami). 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 Auguggcau Duplex with Barium Ions (Model 2), PDB code: 8ami:

Sodium binding site 1 out of 1 in the Crystal Structure of Auguggcau Duplex with Barium Ions (Model 2)


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 Auguggcau Duplex with Barium Ions (Model 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:47.5 occ:1.00 O6 B:G5 2.2 26.8 0.3 O A:HOH202 2.2 24.7 1.0 N7 A:G5 2.4 31.3 1.0 O6 A:G5 2.4 29.6 1.0 N7 B:G5 2.6 33.7 0.7 O6 B:G5 2.7 21.1 0.7 C6 A:G5 2.9 32.5 1.0 C5 A:G5 2.9 30.9 1.0 C6 B:G5 3.0 29.8 0.3 C5 A:G6 3.1 22.5 1.0 N7 B:G5 3.1 31.3 0.3 C6 A:G6 3.1 25.2 1.0 N7 A:G6 3.2 22.1 1.0 O6 A:G6 3.2 23.1 1.0 C5 B:G5 3.3 31.9 0.7 C6 B:G5 3.3 29.8 0.7 C5 B:G5 3.3 30.4 0.3 C6 B:G6 3.5 22.4 1.0 O6 B:G6 3.5 19.2 1.0 C8 A:G5 3.6 33.1 1.0 C5 B:G6 3.7 22.6 1.0 C8 B:G5 3.8 35.3 0.7 C4 A:G6 3.8 26.7 1.0 C8 A:G6 3.9 24.8 1.0 N1 A:G6 3.9 28.4 1.0 N7 B:G6 3.9 23.4 1.0 N1 B:G6 4.1 19.2 1.0 BA A:BA101 4.2 22.2 1.0 C4 A:G5 4.2 30.3 1.0 N1 A:G5 4.3 36.2 1.0 N1 B:G5 4.3 31.6 0.3 O A:HOH215 4.3 19.5 1.0 N9 A:G6 4.3 28.3 1.0 C4 B:G6 4.3 25.6 1.0 C8 B:G5 4.4 32.8 0.3 C2 A:G6 4.6 28.5 1.0 N9 A:G5 4.6 33.4 1.0 C4 B:G5 4.6 33.5 0.7 N3 A:G6 4.6 28.9 1.0 BA B:BA101 4.6 21.8 1.0 C8 B:G6 4.6 26.7 1.0 N1 B:G5 4.7 34.1 0.7 C4 B:G5 4.7 31.6 0.3 C2 B:G6 4.7 20.9 1.0 N9 B:G5 4.8 34.7 0.7 N3 B:G6 4.9 23.4 1.0 N9 B:G6 4.9 28.1 1.0 N3 A:U4 4.9 21.4 1.0 O B:HOH221 5.0 31.2 1.0

A.Kiliszek, M.Pluta, M.Bejger, W.Rypniewski. Structure and Thermodynamics of A Ugg Motif Interacting with BA2+ and Other Metal Ions: Accommodating Changes in the Rna Structure and the Presence of A G(Syn)-G(Syn) Pair. Rna 2022.
ISSN: ESSN 1469-9001
PubMed: 36319090
DOI: 10.1261/RNA.079414.122