Sodium in PDB 1j8g: X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution

The structure of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution, PDB code: 1j8g was solved by J.Deng, Y.Xiong, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.61
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	36.154, 36.154, 74.134, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / 11.2

The structure of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution also contains other interesting chemical elements:

Strontium	(Sr)	8 atoms
Calcium	(Ca)	3 atoms

The binding sites of Sodium atom in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution (pdb code 1j8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution, PDB code: 1j8g:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:8.0 occ:0.41 NA A:NA512 0.0 8.0 0.4 NA A:NA512 1.6 32.9 0.6 O4 A:U6 2.3 5.2 1.0 C4 A:U6 3.2 4.7 1.0 N3 A:U6 3.5 4.6 1.0 O6 A:G5 4.1 3.0 1.0 C5 A:U6 4.5 4.8 1.0 C6 A:G5 4.6 3.0 1.0 C2 A:U6 4.7 4.5 1.0 N1 A:G5 4.8 3.1 1.0 SR A:SR505 4.9 2.6 0.2

Sodium binding site 2 out of 3 in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:32.9 occ:0.58 NA A:NA512 0.0 32.9 0.6 NA A:NA512 1.6 8.0 0.4 O4 A:U6 2.6 5.2 1.0 O6 A:G5 2.9 3.0 1.0 SR A:SR505 3.2 2.6 0.2 C4 A:U6 3.6 4.7 1.0 C6 A:G5 3.6 3.0 1.0 N3 A:U6 3.8 4.6 1.0 N1 A:G5 4.0 3.1 1.0 C5 A:G5 4.7 3.1 1.0 C5 A:U6 4.9 4.8 1.0

Sodium binding site 3 out of 3 in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na513 b:5.9 occ:0.25 O4 B:U16 2.4 3.7 1.0 O B:HOH101 2.4 6.5 0.2 C4 B:U16 3.3 3.4 1.0 N3 B:U16 3.6 3.9 1.0 O6 B:G15 3.6 2.6 1.0 C6 B:G15 4.1 2.4 1.0 SR B:SR507 4.2 2.2 0.2 O B:HOH170 4.4 14.0 1.0 N1 B:G15 4.4 2.5 1.0 C5 B:U16 4.6 3.7 1.0 C2 B:U16 4.9 4.0 1.0

J.Deng, Y.Xiong, M.Sundaralingam. X-Ray Analysis of An Rna Tetraplex (Uggggu)(4) with Divalent Sr(2+) Ions at Subatomic Resolution (0.61 A). Proc.Natl.Acad.Sci.Usa V. 98 13665 2001.
ISSN: ISSN 0027-8424
PubMed: 11707581
DOI: 10.1073/PNAS.241374798