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

Protein crystallography data

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

Other elements in 1j8g:

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

Sodium Binding Sites:

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 1j8g

Go back to Sodium Binding Sites List in 1j8g
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 1j8g

Go back to Sodium Binding Sites List in 1j8g
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 1j8g

Go back to Sodium Binding Sites List in 1j8g
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

Reference:

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
Page generated: Sun Oct 6 18:53:52 2024

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