Calcium 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
Sodium	(Na)	3 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca511 b:6.6 occ:1.00 O A:HOH185 2.2 46.1 0.8 O A:HOH191 2.6 12.3 0.5 O A:HOH206 2.6 18.1 1.0 O A:HOH201 2.7 8.4 0.6 O2' A:U6 2.8 6.7 1.0 O3' A:U6 2.8 7.5 1.0 O A:HOH157 2.8 9.9 1.0 O A:HOH201 3.1 7.1 0.4 C2' A:U6 3.7 5.3 1.0 C3' A:U6 3.8 6.4 1.0 OP2 A:G5 3.9 6.3 1.0 C1' A:U6 4.3 5.0 1.0 O A:HOH191 4.5 20.1 0.5 O2 A:U6 4.6 5.2 1.0 O A:HOH150 4.7 29.8 1.0 O A:HOH123 4.7 4.1 0.5 OP2 A:G4 4.7 5.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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 B:Ca510 b:3.3 occ:1.00 OP1 B:G13 2.5 3.8 1.0 P B:G13 3.8 2.8 1.0 O3' B:G12 3.9 3.2 1.0 O A:HOH164 4.2 6.9 1.0 O C:HOH184 4.4 24.4 0.7 OP2 B:G13 4.8 3.6 1.0 OP1 B:G12 4.8 5.6 1.0 O C:HOH184 4.9 6.8 0.3 O5' B:G13 5.0 3.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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 C:Ca509 b:3.9 occ:1.00 O C:HOH200 2.5 7.5 0.3 O3' C:U26 2.6 7.2 1.0 O C:HOH199 2.6 15.0 0.8 O2' C:U26 2.7 5.0 1.0 O C:HOH198 2.9 5.8 0.5 C2' C:U26 3.6 4.8 1.0 C3' C:U26 3.6 5.9 1.0 OP2 C:G25 4.0 4.2 1.0 O C:HOH133 4.1 4.7 1.0 C1' C:U26 4.1 5.1 1.0 OP1 D:G32 4.3 4.3 1.0 O C:HOH161 4.5 18.1 1.0 O2 C:U26 4.7 7.7 1.0 OP2 C:G24 4.7 3.6 1.0 C4' C:U26 4.8 6.3 1.0 O C:HOH179 5.0 3.2 0.2 O D:HOH142 5.0 16.3 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