Sodium in PDB 6xus: Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base

The structure of Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base, PDB code: 6xus was solved by E.Ennifar, R.Micura, C.Gasser, K.Brillet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	41.12, 35.14, 31.87, 90, 129.43, 90
R / Rfree (%)	15.3 / 17.4

The structure of Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base (pdb code 6xus). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base, PDB code: 6xus:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:14.2 occ:0.35 O A:HOH1274 2.2 36.5 1.0 O A:HOH1300 2.3 41.3 1.0 O A:HOH1253 2.3 23.6 1.0 H41 A:C1003 3.6 14.8 1.0 O A:HOH1237 4.2 23.9 1.0 N4 A:C1003 4.3 12.3 1.0 O A:HOH1265 4.3 20.7 1.0 H62 A:A1005 4.5 19.1 1.0 H61 A:A1005 4.6 19.1 1.0 H42 A:C1003 4.6 14.8 1.0 H5 A:C1003 4.6 16.0 1.0 O A:HOH1239 4.7 33.7 1.0 N6 A:A1005 4.9 15.9 1.0

Sodium binding site 2 out of 2 in the Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:52.1 occ:1.00 OP1 A:U1008 2.4 17.7 1.0 O A:HOH1227 3.5 28.3 0.8 P A:U1008 3.5 16.5 1.0 O A:HOH1218 3.8 51.4 0.9 O A:HOH1214 3.9 31.9 0.8 OP2 A:U1008 4.0 17.2 1.0 O3' A:U1007 4.1 14.9 1.0 O5' A:U1008 4.8 16.2 1.0 H5'' A:U1008 4.9 20.6 1.0 H5'' A:U1007 4.9 17.1 1.0

C.Gasser, I.Delazer, K.Pascher, K.Brillet, S.Klotz, M.Himmelsoss, E.Ennifar, D.Rieder, A.Lusser, R.Micura. Rna Dodecamer with A 6-Hydrazino-2-Aminopurine Modified Base To Be Published.