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Barium 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
Sodium (Na) 8 atoms

Barium Binding Sites:

The binding sites of Barium 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 Barium atom.
In total 8 binding sites of Barium 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 Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Barium binding site 1 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba105

b:6.3
occ:0.25
O6 A:G5 2.7 5.9 1.0
O6 A:G4 2.8 4.8 1.0
C6 A:G4 3.6 4.5 1.0
C6 A:G5 3.7 5.7 1.0
N1 A:G4 3.9 5.0 1.0
N1 A:G5 4.0 5.6 1.0
BA A:BA108 4.4 41.0 0.2
C5 A:G4 4.9 5.2 1.0
C5 A:G5 5.0 6.2 1.0

Barium binding site 2 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba108

b:41.0
occ:0.25
O A:HOH387 2.4 18.1 0.2
O4 A:U6 2.4 8.9 1.0
C4 A:U6 3.3 10.0 1.0
N3 A:U6 3.6 10.4 1.0
O6 A:G5 3.7 5.9 1.0
C6 A:G5 4.2 5.7 1.0
BA A:BA105 4.4 6.3 0.2
N1 A:G5 4.5 5.6 1.0
C5 A:U6 4.6 10.4 1.0
C2 A:U6 4.8 11.4 1.0

Barium binding site 3 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba103

b:5.2
occ:0.25
O6 B:G10 2.7 5.8 1.0
O6 B:G11 2.7 7.9 1.0
NA B:NA207 3.3 27.2 0.2
C6 B:G10 3.6 6.2 1.0
C6 B:G11 3.7 7.8 1.0
N1 B:G10 3.9 5.9 1.0
N1 B:G11 4.0 7.5 1.0
C5 B:G10 4.8 6.8 1.0
O4 B:U12 4.9 12.1 1.0
C5 B:G11 5.0 7.7 1.0

Barium binding site 4 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba104

b:3.1
occ:0.25
O4 B:BRU7 2.6 6.2 1.0
NA C:NA209 2.6 34.1 0.2
O6 B:G8 3.0 5.8 1.0
C4 B:BRU7 3.7 6.9 1.0
C6 B:G8 3.9 4.5 1.0
NA B:NA202 4.0 14.4 0.2
N1 B:G8 4.2 4.6 1.0
N3 B:BRU7 4.3 6.3 1.0

Barium binding site 5 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba101

b:2.7
occ:0.25
O6 C:G16 2.7 4.5 1.0
O6 C:G17 2.7 4.0 1.0
NA C:NA201 3.1 14.5 0.2
C6 C:G16 3.6 4.2 1.0
C6 C:G17 3.7 4.5 1.0
N1 C:G16 3.9 4.5 1.0
N1 C:G17 4.0 4.5 1.0
C5 C:G16 4.9 4.2 1.0

Barium binding site 6 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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:Ba106

b:13.9
occ:0.25
O3' C:U18 2.8 13.6 1.0
O C:HOH371 2.8 21.6 1.0
O2' C:U18 2.9 12.0 1.0
O C:HOH313 2.9 14.8 1.0
O C:HOH369 3.1 23.9 1.0
C2' C:U18 3.6 12.0 1.0
C3' C:U18 3.7 12.1 1.0
OP2 C:G17 3.9 9.3 1.0
C1' C:U18 4.4 11.6 1.0
O2 C:U18 4.9 9.6 1.0
C4' C:U18 5.0 11.9 1.0

Barium binding site 7 out of 8 in 1j6s

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Barium 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 Barium with other atoms in the Ba 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
D:Ba102

b:3.8
occ:0.25
O6 D:G23 2.8 5.1 1.0
O6 D:G22 2.8 5.9 1.0
C6 D:G22 3.6 5.8 1.0
C6 D:G23 3.7 5.1 1.0
N1 D:G22 3.9 5.7 1.0
N1 D:G23 4.0 5.3 1.0
C5 D:G22 4.8 6.3 1.0

Barium binding site 8 out of 8 in 1j6s

Go back to Barium Binding Sites List in 1j6s
Barium 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 Barium with other atoms in the Ba 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:Ba107

b:2.1
occ:0.25
O6 D:G20 2.8 4.1 1.0
O4 D:BRU19 2.8 5.8 1.0
C6 D:G20 3.7 5.3 1.0
NA D:NA208 3.8 13.4 0.2
C4 D:BRU19 3.9 5.9 1.0
N1 D:G20 4.1 4.8 1.0
N3 D:BRU19 4.3 6.0 1.0
C5 D:G20 4.9 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: Wed Jul 10 14:58:12 2024

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