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Sodium in PDB 1j6s: Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads

Protein crystallography data

The structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads, PDB code: 1j6s was solved by B.Pan, Y.Xiong, K.Shi, J.Deng, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 37.984, 37.984, 82.195, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.4

Other elements in 1j6s:

The structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Barium (Ba) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads (pdb code 1j6s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads, PDB code: 1j6s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1j6s

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Sodium binding site 1 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


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 Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:35.8
occ:0.25
O6 A:G2 3.0 5.5 1.0
NA A:NA206 3.5 10.1 0.2
C6 A:G2 3.8 4.7 1.0
N1 A:G2 4.0 5.0 1.0
C5 A:G2 5.0 4.3 1.0

Sodium binding site 2 out of 8 in 1j6s

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Sodium binding site 2 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:10.1
occ:0.25
O6 A:G2 2.9 5.5 1.0
N6 A:A3 3.3 5.3 1.0
NA A:NA205 3.5 35.8 0.2
C6 A:G2 3.8 4.7 1.0
N1 A:G2 4.0 5.0 1.0
C6 A:A3 4.3 4.8 1.0
N7 A:A3 4.6 5.0 1.0
C5 A:A3 4.8 5.0 1.0

Sodium binding site 3 out of 8 in 1j6s

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Sodium binding site 3 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:14.4
occ:0.25
O6 B:G8 3.1 5.8 1.0
N6 B:A9 3.2 6.7 1.0
C6 B:G8 3.9 4.5 1.0
BA B:BA104 4.0 3.1 0.2
N1 B:G8 4.1 4.6 1.0
C6 B:A9 4.3 6.0 1.0
N7 B:A9 4.5 7.2 1.0
C5 B:A9 4.8 6.1 1.0

Sodium binding site 4 out of 8 in 1j6s

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Sodium binding site 4 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:27.2
occ:0.25
O4 B:U12 2.5 12.1 1.0
O6 B:G11 3.0 7.9 1.0
BA B:BA103 3.3 5.2 0.2
C4 B:U12 3.5 12.5 1.0
C6 B:G11 3.7 7.8 1.0
N3 B:U12 3.8 12.7 1.0
N1 B:G11 4.0 7.5 1.0
C5 B:G11 4.8 7.7 1.0
C5 B:U12 4.8 12.9 1.0

Sodium binding site 5 out of 8 in 1j6s

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Sodium binding site 5 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:14.5
occ:0.25
O4 C:U18 2.9 9.0 1.0
O6 C:G17 2.9 4.0 1.0
BA C:BA101 3.1 2.7 0.2
C6 C:G17 3.6 4.5 1.0
C4 C:U18 3.8 9.4 1.0
N1 C:G17 3.9 4.5 1.0
N3 C:U18 3.9 9.5 1.0
C5 C:G17 4.8 4.7 1.0

Sodium binding site 6 out of 8 in 1j6s

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Sodium binding site 6 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:11.2
occ:0.25
O6 C:G14 3.0 6.2 1.0
N6 C:A15 3.2 5.5 1.0
C6 C:G14 3.8 5.6 1.0
NA C:NA209 4.0 34.1 0.2
N1 C:G14 4.1 5.1 1.0
C6 C:A15 4.3 5.4 1.0
N7 C:A15 4.4 6.2 1.0
C5 C:A15 4.7 5.8 1.0

Sodium binding site 7 out of 8 in 1j6s

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Sodium binding site 7 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na209

b:34.1
occ:0.25
BA B:BA104 2.6 3.1 0.2
O4 B:BRU7 3.0 6.2 1.0
O6 C:G14 3.1 6.2 1.0
C4 B:BRU7 3.9 6.9 1.0
C6 C:G14 4.0 5.6 1.0
NA C:NA203 4.0 11.2 0.2
N1 C:G14 4.2 5.1 1.0
N3 B:BRU7 4.4 6.3 1.0

Sodium binding site 8 out of 8 in 1j6s

Go back to Sodium Binding Sites List in 1j6s
Sodium binding site 8 out of 8 in the Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of An Rna Tetraplex (Ugaggu)4 with A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na208

b:13.4
occ:0.25
O6 D:G20 3.0 4.1 1.0
N6 D:A21 3.2 7.1 1.0
C6 D:G20 3.8 5.3 1.0
BA D:BA107 3.8 2.1 0.2
N1 D:G20 4.1 4.8 1.0
C6 D:A21 4.3 7.1 1.0
N7 D:A21 4.5 6.4 1.0
C5 D:A21 4.7 7.1 1.0
C5 D:G20 5.0 5.4 1.0

Reference:

B.Pan, Y.Xiong, K.Shi, J.Deng, M.Sundaralingam. Crystal Structure of An Rna Purine-Rich Tetraplex Containing Adenine Tetrads: Implications For Specific Binding in Rna Tetraplexes Structure V. 11 815 2003.
ISSN: ISSN 0969-2126
PubMed: 12842044
DOI: 10.1016/S0969-2126(03)00107-2
Page generated: Tue Dec 15 05:25:56 2020

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