Sodium in PDB 7qua: Duplex Rna Containing Xanthosine-Cytosine Base Pairs

The structure of Duplex Rna Containing Xanthosine-Cytosine Base Pairs, PDB code: 7qua was solved by E.Ennifar, R.Micura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.80 / 1.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	41.07, 35.15, 31.93, 90, 129.05, 90
R / Rfree (%)	13.7 / 15.8

The structure of Duplex Rna Containing Xanthosine-Cytosine Base Pairs also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs (pdb code 7qua). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs, PDB code: 7qua:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Duplex Rna Containing Xanthosine-Cytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:10.6 occ:0.72 O A:HOH1278 2.3 26.9 1.0 O A:HOH1282 2.3 13.7 1.0 O4 A:U1007 2.4 8.4 1.0 O A:HOH1279 2.4 19.9 1.0 O4 A:U1008 2.5 9.2 1.0 C4 A:U1007 3.2 8.5 1.0 C4 A:U1008 3.6 9.1 1.0 H5 A:U1007 3.8 10.6 1.0 H62 A:A1009 3.9 10.1 1.0 C5 A:U1007 3.9 8.9 1.0 H5 A:U1008 3.9 11.9 1.0 H61 A:A1009 4.0 10.1 1.0 N6 A:A1009 4.2 8.5 1.0 N3 A:U1007 4.2 8.8 1.0 H3 A:U1007 4.2 10.6 1.0 C5 A:U1008 4.2 9.9 1.0 O A:HOH1233 4.6 21.7 1.0 N3 A:U1008 4.7 9.3 1.0 H3 A:U1008 4.8 11.2 1.0 O A:HOH1253 4.8 14.3 1.0 H62 A:A1006 5.0 10.2 1.0 O A:HOH1242 5.0 23.4 1.0

Sodium binding site 2 out of 2 in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Duplex Rna Containing Xanthosine-Cytosine Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:29.0 occ:1.00 O A:HOH1268 2.3 24.5 1.0 O A:HOH1298 2.3 36.7 1.0 O A:HOH1260 2.6 19.1 1.0 O A:HOH1305 2.9 34.2 1.0 H41 A:C1003 3.3 10.4 1.0 O A:HOH1201 3.5 35.8 1.0 O A:HOH1230 3.6 16.9 1.0 H5 A:C1003 3.7 10.9 1.0 N4 A:C1003 3.9 8.7 1.0 C5 A:C1003 4.3 9.1 1.0 O A:HOH1234 4.3 26.6 1.0 O6 A:XMP1005 4.4 9.2 1.0 H42 A:C1003 4.4 10.4 1.0 C4 A:C1003 4.4 8.5 1.0 O A:HOH1304 4.6 33.2 1.0 O6 A:G1004 4.8 7.9 1.0 O A:HOH1249 4.9 22.0 1.0

S.Mair, K.Erharter, E.Renard, K.Brillet, M.Brunner, A.Lusser, C.Kreutz, E.Ennifar, R.Micura. Synthesis and Properties of Xanthosine-Modified Rna To Be Published.