Atomistry » Sodium » PDB 1hnf-1jay » 1j6s
Atomistry »
  Sodium »
    PDB 1hnf-1jay »
      1j6s »

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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Go back to Sodium Binding Sites List in 1j6s
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy