Sodium in PDB 437d: Crystal Structure of An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting

The structure of Crystal Structure of An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting, PDB code: 437d was solved by L.Su, L.Chen, M.Egli, J.M.Berger, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	30.080, 30.080, 140.080, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.4

The structure of Crystal Structure of An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting (pdb code 437d). 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 An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting, PDB code: 437d:

Sodium binding site 1 out of 1 in the Crystal Structure of An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting


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 An Rna Pseudoknot From Beet Western Yellow Virus Involved in Ribosomal Frameshifting within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:22.9 occ:1.00 OP2 A:A21 2.6 20.7 1.0 O A:HOH149 2.8 35.5 1.0 N3 A:G16 2.8 18.0 1.0 O2' A:G16 2.8 22.2 1.0 N7 A:A21 2.9 24.6 1.0 C8 A:A21 3.3 30.4 1.0 C2' A:G16 3.4 23.2 1.0 O4' A:C17 3.6 25.4 1.0 C1' A:G16 3.6 20.6 1.0 N2 A:G16 3.6 16.5 1.0 C2 A:G16 3.6 19.4 1.0 O A:HOH130 3.7 33.0 1.0 C4 A:G16 3.8 15.0 1.0 P A:A21 3.9 22.1 1.0 C1' A:C17 4.0 20.2 1.0 N9 A:G16 4.1 24.0 1.0 O5' A:A21 4.1 23.8 1.0 C5 A:A21 4.2 31.0 1.0 O3' A:A20 4.4 19.0 1.0 N2 A:G6 4.4 19.6 1.0 C4' A:C17 4.5 22.8 1.0 O2' A:C17 4.5 24.3 1.0 N3 A:G6 4.6 16.9 1.0 N9 A:A21 4.6 22.9 1.0 N4 A:C22 4.7 32.5 1.0 C2 A:G6 4.7 22.6 1.0 O4' A:G16 4.9 19.7 1.0 C3' A:G16 4.9 25.2 1.0 C5 A:C22 4.9 35.3 1.0 O2' A:A20 4.9 21.1 1.0 C2' A:C17 4.9 15.8 1.0 N1 A:G16 4.9 18.8 1.0 N6 A:A21 5.0 31.6 1.0 N1 A:C17 5.0 18.8 1.0

L.Su, L.Chen, M.Egli, J.M.Berger, A.Rich. Minor Groove Rna Triplex in the Crystal Structure of A Ribosomal Frameshifting Viral Pseudoknot. Nat.Struct.Biol. V. 6 285 1999.
ISSN: ISSN 1072-8368
PubMed: 10074948
DOI: 10.1038/6722