Sodium in PDB 2r1s: Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1), PDB code: 2r1s was solved by Y.Timsit, S.Bombard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.10 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.380, 25.670, 29.920, 98.64, 105.43, 100.67
R / Rfree (%)	15.9 / 18.5

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) (pdb code 2r1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1), PDB code: 2r1s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na14 b:12.5 occ:0.97 O A:HOH37 2.3 17.7 1.0 O A:HOH50 2.4 16.1 1.0 O4 A:U5 2.4 6.9 1.0 O A:HOH59 2.4 16.1 1.0 O A:HOH56 2.5 13.6 1.0 O4 A:U4 2.5 7.2 1.0 C4 A:U4 3.3 6.2 1.0 C4 A:U5 3.4 5.6 1.0 O A:HOH84 3.5 29.2 1.0 C5 A:U4 3.7 5.5 1.0 C5 A:U5 4.0 6.3 1.0 N6 B:A22 4.1 7.4 1.0 O A:HOH25 4.3 11.4 1.0 O A:HOH58 4.3 17.4 1.0 O A:HOH26 4.4 10.2 1.0 N3 A:U4 4.4 5.8 1.0 N6 B:A23 4.4 5.9 1.0 O A:HOH20 4.5 12.4 1.0 N3 A:U5 4.5 5.9 1.0 O B:HOH75 4.6 25.3 1.0 O A:HOH21 4.9 12.3 1.0 C6 A:U4 5.0 5.7 1.0

Sodium binding site 2 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na15 b:20.4 occ:0.97 N7 A:G7 2.5 8.1 1.0 O A:HOH31 2.5 12.5 1.0 O A:HOH52 2.5 20.2 1.0 O A:HOH76 2.5 29.4 0.9 O A:HOH72 2.6 17.5 1.0 O A:HOH61 2.7 23.6 0.9 C8 A:G7 3.2 8.8 1.0 C5 A:G7 3.5 7.0 1.0 O A:HOH75 3.9 24.7 1.0 O6 A:G7 4.0 8.5 1.0 C6 A:G7 4.1 7.1 1.0 OP2 A:G7 4.3 8.7 1.0 N9 A:G7 4.3 7.4 1.0 C4 A:G7 4.5 7.4 1.0 C5 A:5BU6 4.5 7.1 1.0 BR A:5BU6 4.6 11.0 1.0 O A:HOH100 4.7 34.6 1.0 C4 A:5BU6 4.8 7.9 1.0 OP2 A:A8 4.8 12.8 1.0 O5' A:G7 4.8 8.4 1.0 C6 A:5BU6 4.9 8.6 1.0

Sodium binding site 3 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na16 b:17.4 occ:0.92 O A:HOH85 2.2 24.8 1.0 O A:HOH102 2.4 25.2 1.0 O A:HOH53 2.5 14.4 1.0 N7 A:A9 2.6 6.5 1.0 O A:HOH71 2.6 17.2 1.0 O A:HOH88 2.6 34.7 1.0 C8 A:A9 3.4 6.0 1.0 C5 A:A9 3.6 6.4 1.0 N6 A:A9 3.8 6.8 1.0 O A:HOH81 3.9 16.4 1.0 OP2 A:A9 4.0 9.4 1.0 C6 A:A9 4.1 6.4 1.0 O B:HOH65 4.5 13.6 1.0 O A:HOH100 4.5 34.6 1.0 N7 A:A8 4.5 6.5 1.0 N9 A:A9 4.6 5.6 1.0 C4 A:A9 4.7 5.8 1.0 O B:HOH96 4.8 28.0 0.9 O A:HOH61 4.8 23.6 0.9 O A:HOH75 4.8 24.7 1.0 C8 A:A8 4.9 6.5 1.0 C5 A:A8 4.9 6.2 1.0

Sodium binding site 4 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:11.1 occ:0.98 O4 B:U18 2.4 5.8 1.0 O B:HOH65 2.4 13.6 1.0 O B:HOH66 2.4 14.8 1.0 O B:HOH44 2.4 15.1 1.0 O4 B:U17 2.5 10.0 1.0 O B:HOH67 2.5 13.1 1.0 C4 B:U18 3.3 5.0 1.0 C4 B:U17 3.4 8.7 1.0 NA B:NA4 3.6 25.8 0.9 C5 B:U17 3.8 8.3 1.0 C5 B:U18 3.9 5.3 1.0 N6 A:A9 4.0 6.8 1.0 O B:HOH48 4.2 13.0 1.0 O B:HOH76 4.3 17.9 1.0 N6 A:A10 4.4 7.7 1.0 O B:HOH36 4.4 14.2 1.0 O B:HOH49 4.5 17.7 1.0 N3 B:U18 4.5 5.3 1.0 N3 B:U17 4.5 7.8 1.0 O B:HOH38 4.5 13.7 1.0 O A:HOH75 4.7 24.7 1.0 O A:HOH102 4.7 25.2 1.0 O B:HOH37 4.9 12.4 1.0

Sodium binding site 5 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.4 A (BR1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4 b:25.8 occ:0.93 O B:HOH108 2.3 35.5 0.8 O B:HOH66 2.3 14.8 1.0 O B:HOH38 2.4 13.7 1.0 O B:HOH107 2.4 27.6 1.0 O B:HOH67 2.4 13.1 1.0 NA B:NA1 3.6 11.1 1.0 O B:HOH37 4.0 12.4 1.0 O B:HOH98 4.1 26.1 0.8 OP2 B:G16 4.1 10.7 1.0 O B:HOH44 4.2 15.1 1.0 OP2 B:U17 4.4 9.3 1.0 O B:HOH76 4.5 17.9 1.0 O B:HOH49 4.7 17.7 1.0 C5 B:U17 4.9 8.3 1.0

Y.Timsit, S.Bombard. The 1.3 A Resolution Structure of the Rna Tridecamer R(Gcguuugaaacgc): Metal Ion Binding Correlates with Base Unstacking and Groove Contraction. Rna V. 13 2098 2007.
ISSN: ISSN 1355-8382
PubMed: 17940138
DOI: 10.1261/RNA.730207