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Strontium 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:

Calcium (Ca) 3 atoms
Sodium (Na) 3 atoms

Strontium Binding Sites:

The binding sites of Strontium 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 Strontium atom.
In total 8 binding sites of Strontium where determined in the X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 at Ultra-High Resolution, PDB code: 1j8g:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 1j8g

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Strontium binding site 1 out of 8 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 Strontium with other atoms in the Sr 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:Sr505

b:2.6
occ:0.25
 O6 A:G4 2.6 2.5 1.0
O6 A:G5 2.6 3.0 1.0
NA A:NA512 3.2 32.9 0.6
C6 A:G4 3.5 2.3 1.0
C6 A:G5 3.6 3.0 1.0
N1 A:G4 3.9 2.4 1.0
N1 A:G5 4.0 3.1 1.0
C5 A:G4 4.8 2.4 1.0
NA A:NA512 4.9 8.0 0.4
C5 A:G5 4.9 3.1 1.0

Strontium binding site 2 out of 8 in 1j8g

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Strontium binding site 2 out of 8 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 Strontium with other atoms in the Sr 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:Sr506

b:1.9
occ:0.25
 O6 A:G2 2.6 2.2 1.0
O6 A:G3 2.6 2.2 1.0
C6 A:G2 3.6 2.0 1.0
C6 A:G3 3.6 2.0 1.0
N1 A:G2 3.9 2.1 1.0
N1 A:G3 4.0 2.1 1.0
C5 A:G2 4.8 2.1 1.0
C5 A:G3 4.9 2.1 1.0

Strontium binding site 3 out of 8 in 1j8g

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Strontium binding site 3 out of 8 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 Strontium with other atoms in the Sr 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:Sr502

b:1.9
occ:0.25
 O6 B:G12 2.6 2.1 1.0
O6 B:G13 2.6 2.1 1.0
C6 B:G12 3.6 2.1 1.0
C6 B:G13 3.6 1.9 1.0
N1 B:G12 3.9 2.2 1.0
N1 B:G13 4.0 2.0 1.0
C5 B:G12 4.8 2.3 1.0
C5 B:G13 4.9 2.0 1.0

Strontium binding site 4 out of 8 in 1j8g

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Strontium binding site 4 out of 8 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 Strontium with other atoms in the Sr binding site number 4 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:Sr507

b:2.2
occ:0.25
 O6 B:G15 2.6 2.6 1.0
O6 B:G14 2.6 2.2 1.0
C6 B:G14 3.5 1.8 1.0
C6 B:G15 3.6 2.4 1.0
N1 B:G14 3.9 2.0 1.0
N1 B:G15 4.0 2.5 1.0
NA B:NA513 4.2 5.9 0.2
C5 B:G14 4.8 2.1 1.0
C5 B:G15 4.9 2.5 1.0

Strontium binding site 5 out of 8 in 1j8g

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Strontium binding site 5 out of 8 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 Strontium with other atoms in the Sr binding site number 5 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:Sr503

b:1.9
occ:0.25
 O6 C:G23 2.6 2.0 1.0
O6 C:G22 2.6 2.1 1.0
C6 C:G22 3.6 2.0 1.0
C6 C:G23 3.6 1.9 1.0
N1 C:G22 3.9 2.0 1.0
N1 C:G23 4.0 2.0 1.0
C5 C:G22 4.8 2.1 1.0
C5 C:G23 4.9 2.0 1.0

Strontium binding site 6 out of 8 in 1j8g

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Strontium binding site 6 out of 8 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 Strontium with other atoms in the Sr binding site number 6 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:Sr504

b:3.3
occ:0.25
 O6 C:G25 2.6 3.0 1.0
O6 C:G24 2.7 2.4 1.0
O C:HOH102 2.8 5.3 0.2
C6 C:G24 3.6 2.2 1.0
C6 C:G25 3.6 2.9 1.0
N1 C:G24 3.9 2.3 1.0
N1 C:G25 4.0 3.0 1.0
C5 C:G24 4.8 2.2 1.0
C5 C:G25 4.9 3.0 1.0

Strontium binding site 7 out of 8 in 1j8g

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Strontium binding site 7 out of 8 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 Strontium with other atoms in the Sr binding site number 7 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
D:Sr501

b:3.2
occ:0.25
 O6 D:G35 2.6 3.7 1.0
O6 D:G34 2.6 3.2 1.0
C6 D:G34 3.5 3.0 1.0
C6 D:G35 3.6 3.8 1.0
N1 D:G34 3.9 3.1 1.0
N1 D:G35 4.0 4.0 1.0
C5 D:G34 4.8 3.2 1.0
O D:HOH95 4.9 11.7 0.6
C5 D:G35 4.9 4.0 1.0

Strontium binding site 8 out of 8 in 1j8g

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Strontium binding site 8 out of 8 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 Strontium with other atoms in the Sr binding site number 8 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
D:Sr508

b:2.3
occ:0.25
 O6 D:G32 2.6 2.5 1.0
O6 D:G33 2.6 2.6 1.0
C6 D:G32 3.6 2.3 1.0
C6 D:G33 3.6 2.5 1.0
N1 D:G32 3.9 2.4 1.0
N1 D:G33 4.0 2.6 1.0
C5 D:G32 4.8 2.5 1.0
C5 D:G33 4.9 2.9 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: Thu Oct 10 14:03:40 2024

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