Sodium in PDB 5lqt: Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.58 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	34.340, 34.340, 103.170, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 22.7

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Bromine	(Br)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs (pdb code 5lqt). 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 Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs, PDB code: 5lqt:

Sodium binding site 1 out of 1 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-C Basepairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:60.2 occ:1.00 O2 A:CBV2 2.6 33.8 1.0 O B:HOH207 3.0 34.1 1.0 O A:HOH228 3.0 54.0 1.0 C2 A:CBV2 3.6 30.7 1.0 O2' A:CBV2 3.6 33.7 1.0 C1' A:CBV2 3.7 31.3 1.0 N2 B:G9 3.9 32.4 1.0 O A:HOH220 3.9 45.2 1.0 C2' A:CBV2 4.0 32.2 1.0 O2 B:C10 4.1 28.3 1.0 N2 A:G1 4.1 29.5 1.0 N1 A:CBV2 4.2 25.8 1.0 N3 A:CBV2 4.8 28.4 1.0 O4' A:CBV2 4.8 32.0 1.0 O4' A:C3 4.9 29.3 1.0

L.Huang, S.Ashraf, J.Wang, D.M.Lilley. Control of Box C/D Snornp Assembly By N(6)-Methylation of Adenine. Embo Rep. V. 18 1631 2017.
ISSN: ESSN 1469-3178
PubMed: 28623187
DOI: 10.15252/EMBR.201743967