Sodium in PDB 2r20: Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2)

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2), PDB code: 2r20 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 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.280, 25.800, 29.990, 98.62, 105.58, 100.92
R / Rfree (%)	18.1 / 19.5

The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2) 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 1.3 A (BR2) (pdb code 2r20). 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 1.3 A (BR2), PDB code: 2r20:
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 1.3 A (BR2)


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 1.3 A (BR2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na14 b:17.4 occ:1.00 O A:HOH55 2.4 18.5 1.0 O A:HOH37 2.4 21.5 1.0 O A:HOH58 2.4 22.8 1.0 O4 A:U5 2.4 9.3 1.0 O A:HOH49 2.5 22.1 1.0 O4 A:U4 2.5 9.6 1.0 C4 A:U4 3.3 8.8 1.0 C4 A:U5 3.4 8.4 1.0 C5 A:U4 3.7 7.6 1.0 O A:HOH82 3.8 32.5 1.0 C5 A:U5 4.0 8.7 1.0 N6 B:A22 4.1 10.7 1.0 O A:HOH25 4.4 15.6 1.0 O A:HOH26 4.4 13.9 1.0 N3 A:U4 4.4 8.3 1.0 O A:HOH57 4.4 20.1 1.0 N6 B:A23 4.5 8.6 1.0 O A:HOH20 4.5 16.0 1.0 N3 A:U5 4.5 8.1 1.0 C6 A:U4 4.9 8.7 1.0

Sodium binding site 2 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2)


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 1.3 A (BR2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na15 b:20.7 occ:1.00 O A:HOH75 2.4 35.3 1.0 O A:HOH31 2.4 16.4 1.0 O A:HOH51 2.5 22.1 1.0 N7 A:G7 2.5 10.8 1.0 O A:HOH71 2.6 22.1 1.0 O A:HOH60 2.7 27.3 1.0 C8 A:G7 3.2 11.0 1.0 C5 A:G7 3.5 9.5 1.0 O A:HOH74 3.9 29.8 1.0 O6 A:G7 4.0 10.3 1.0 C6 A:G7 4.1 9.7 1.0 N9 A:G7 4.3 10.6 1.0 OP2 A:G7 4.3 12.4 1.0 C4 A:G7 4.5 9.6 1.0 C5 A:5BU6 4.5 9.9 1.0 BR A:5BU6 4.6 20.0 1.0 OP2 A:A8 4.7 15.3 1.0 C4 A:5BU6 4.8 11.1 1.0 C6 A:5BU6 4.8 11.4 1.0 O5' A:G7 4.9 12.0 1.0 O A:HOH97 4.9 37.4 1.0 N7 A:A8 5.0 9.3 1.0

Sodium binding site 3 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2)


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 1.3 A (BR2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na16 b:25.5 occ:1.00 O A:HOH83 2.2 26.0 1.0 O A:HOH52 2.3 23.7 1.0 O A:HOH99 2.4 30.4 1.0 O A:HOH86 2.6 39.6 1.0 N7 A:A9 2.6 8.2 1.0 O A:HOH70 2.7 25.3 1.0 C8 A:A9 3.5 8.4 1.0 C5 A:A9 3.6 8.4 1.0 N6 A:A9 3.8 9.9 1.0 O A:HOH80 3.9 21.4 1.0 OP2 A:A9 3.9 12.4 1.0 C6 A:A9 4.1 8.8 1.0 O A:HOH97 4.3 37.4 1.0 O B:HOH64 4.4 15.2 1.0 N7 A:A8 4.5 9.3 1.0 O B:HOH94 4.7 28.4 1.0 O A:HOH60 4.7 27.3 1.0 N9 A:A9 4.7 7.5 1.0 C4 A:A9 4.8 8.2 1.0 C8 A:A8 4.9 9.2 1.0 O A:HOH74 4.9 29.8 1.0 C5 A:A8 4.9 8.7 1.0

Sodium binding site 4 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2)


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 1.3 A (BR2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:14.4 occ:1.00 O B:HOH44 2.3 19.9 1.0 O4 B:U18 2.4 9.4 1.0 O B:HOH66 2.4 19.5 1.0 O B:HOH67 2.5 15.5 1.0 O B:HOH64 2.5 15.2 1.0 O4 B:U17 2.5 11.4 1.0 C4 B:U18 3.3 8.5 1.0 C4 B:U17 3.4 9.7 1.0 NA B:NA4 3.7 33.4 1.0 C5 B:U17 3.8 9.8 1.0 C5 B:U18 3.8 8.1 1.0 N6 A:A9 4.1 9.9 1.0 O B:HOH36 4.3 18.6 1.0 O B:HOH73 4.3 22.1 1.0 O B:HOH48 4.4 14.7 1.0 N6 A:A10 4.4 10.1 1.0 N3 B:U18 4.5 8.2 1.0 N3 B:U17 4.5 9.9 1.0 O B:HOH38 4.5 16.9 1.0 O B:HOH49 4.5 17.3 1.0 O A:HOH74 4.6 29.8 1.0 O A:HOH99 4.9 30.4 1.0 O B:HOH37 4.9 14.0 1.0

Sodium binding site 5 out of 5 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.3 A (BR2)


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 1.3 A (BR2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4 b:33.4 occ:1.00 O B:HOH102 2.4 32.1 1.0 O B:HOH38 2.4 16.9 1.0 O B:HOH66 2.5 19.5 1.0 O B:HOH67 2.6 15.5 1.0 NA B:NA1 3.7 14.4 1.0 O B:HOH37 4.0 14.0 1.0 OP2 B:G16 4.1 14.0 1.0 O B:HOH44 4.3 19.9 1.0 OP2 B:U17 4.4 12.4 1.0 O B:HOH73 4.6 22.1 1.0 O B:HOH49 4.8 17.3 1.0 C5 B:U17 4.9 9.8 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