Sodium in PDB 2r21: Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn), PDB code: 2r21 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)	20.00 / 1.59
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.250, 25.650, 29.720, 98.13, 106.15, 100.83
R / Rfree (%)	16.9 / 19.1

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Manganese	(Mn)	1 atom

The binding sites of Sodium atom in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) (pdb code 2r21). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn), PDB code: 2r21:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)


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 1.6 A (Brmn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na14 b:15.2 occ:1.00 O A:HOH89 2.3 24.6 0.8 O A:HOH37 2.3 24.2 1.0 O A:HOH49 2.5 21.5 0.9 O4 A:U4 2.5 9.6 1.0 O4 A:U5 2.5 10.3 1.0 O A:HOH53 2.5 18.8 1.0 O B:HOH73 2.8 28.3 1.0 C4 A:U4 3.3 8.7 1.0 C4 A:U5 3.5 8.5 1.0 C5 A:U4 3.7 7.1 1.0 C5 A:U5 4.1 9.5 1.0 N6 B:A22 4.1 9.9 1.0 O A:HOH20 4.4 15.6 1.0 O A:HOH26 4.4 12.2 1.0 N3 A:U4 4.4 8.2 1.0 O A:HOH55 4.4 24.7 1.0 O A:HOH25 4.4 14.5 1.0 N6 B:A23 4.6 9.9 1.0 N3 A:U5 4.6 9.3 1.0 O A:HOH21 4.9 18.9 1.0 C6 A:U4 4.9 8.3 1.0

Sodium binding site 2 out of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)


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 1.6 A (Brmn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na15 b:18.2 occ:1.00 O A:HOH31 2.5 15.4 1.0 O A:HOH51 2.5 20.3 1.0 O A:HOH71 2.5 28.1 0.9 N7 A:G7 2.6 11.8 1.0 O A:HOH68 2.6 19.2 0.9 O A:HOH58 2.6 20.5 1.0 C8 A:G7 3.3 10.2 1.0 C5 A:G7 3.6 8.9 1.0 O6 A:G7 4.1 11.4 1.0 C6 A:G7 4.2 10.4 1.0 OP2 A:G7 4.2 10.4 1.0 BR A:5BU6 4.4 17.3 1.0 C5 A:5BU6 4.4 11.6 1.0 N9 A:G7 4.4 9.8 1.0 C4 A:G7 4.6 9.0 1.0 C4 A:5BU6 4.7 11.3 1.0 C6 A:5BU6 4.7 10.6 1.0 OP2 A:A8 4.8 14.1 1.0 O5' A:G7 4.9 10.0 1.0

Sodium binding site 3 out of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)


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 1.6 A (Brmn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na16 b:38.5 occ:0.67 O A:HOH92 2.3 34.7 1.0 O A:HOH52 2.5 23.1 0.9 O A:HOH93 2.5 36.7 0.9 N7 A:A9 2.7 7.3 1.0 O A:HOH67 2.9 19.1 1.0 C8 A:A9 3.6 8.5 1.0 C5 A:A9 3.8 8.4 1.0 N6 A:A9 3.9 9.0 1.0 OP2 A:A9 3.9 9.8 1.0 O A:HOH75 4.1 23.0 1.0 C6 A:A9 4.3 7.8 1.0 O B:HOH65 4.5 20.9 1.0 N7 A:A8 4.5 10.4 1.0 O B:HOH89 4.6 28.9 0.8 O A:HOH90 4.8 32.4 1.0 O A:HOH58 4.8 20.5 1.0 N9 A:A9 4.8 7.9 1.0 C8 A:A8 4.9 8.9 1.0 C4 A:A9 4.9 9.1 1.0 C5 A:A8 5.0 8.7 1.0

Sodium binding site 4 out of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)


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 1.6 A (Brmn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:22.4 occ:0.96 O B:HOH65 2.3 20.9 1.0 O4 B:U18 2.4 11.2 1.0 O B:HOH66 2.4 26.6 1.0 O4 B:U17 2.4 12.4 1.0 O B:HOH44 2.5 22.0 1.0 O B:HOH67 2.5 20.0 1.0 C4 B:U17 3.3 12.0 1.0 C4 B:U18 3.3 8.6 1.0 C5 B:U17 3.7 10.6 1.0 C5 B:U18 3.8 9.1 1.0 O B:HOH108 3.8 35.1 1.0 N6 A:A9 4.0 9.0 1.0 O B:HOH48 4.1 18.3 1.0 O B:HOH36 4.3 19.3 1.0 O B:HOH38 4.3 21.6 1.0 N3 B:U17 4.4 10.7 1.0 N3 B:U18 4.4 7.5 1.0 N6 A:A10 4.4 10.9 1.0 O B:HOH49 4.4 23.3 1.0 O A:HOH92 4.6 34.7 1.0 O B:HOH37 5.0 16.4 1.0 C6 B:U17 5.0 10.5 1.0

Y.Timsit, S.Bombard. 1.3 A Resolution Structure of the Tridecamer R(Gcguuugaaacgc) To Be Published.