Sodium in PDB 246d: Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue

The structure of Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue, PDB code: 246d was solved by M.C.Wahl, C.Ban, C.Sekharudu, B.Ramakrishnan, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	43.100, 43.100, 59.400, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / n/a

The binding sites of Sodium atom in the Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue (pdb code 246d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue, PDB code: 246d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue


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 Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue within 5.0Å range: probe atom residue distance (Å) B Occ B:Na17 b:2.0 occ:0.33 O2' B:A11 2.4 26.7 1.0 O B:HOH102 2.5 7.5 0.3 O3' B:A11 3.5 25.4 1.0 C2' B:A11 3.8 19.1 1.0 O B:HOH77 4.1 80.9 1.0 C3' B:A11 4.2 19.6 1.0 C5' B:U12 4.2 22.7 1.0 C4' B:A11 4.2 21.4 1.0 O5' B:U12 4.6 28.2 1.0 P B:U12 4.6 23.6 1.0 OP1 B:U12 4.8 32.7 1.0 C1' B:A11 4.8 19.3 1.0 NA B:NA18 4.8 3.8 0.3 O4' B:U12 4.9 25.6 1.0 O4' B:A11 4.9 22.2 1.0 C4' B:U12 5.0 23.2 1.0

Sodium binding site 2 out of 2 in the Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue


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 Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C) , with A 3'-Terminal Deoxy Residue within 5.0Å range: probe atom residue distance (Å) B Occ B:Na18 b:3.8 occ:0.33 O B:HOH77 2.3 80.9 1.0 O B:HOH23 2.4 46.3 1.0 O A:HOH22 3.8 75.4 1.0 O B:HOH62 3.9 43.6 1.0 O2' B:A11 4.4 26.7 1.0 NA B:NA17 4.8 2.0 0.3 O A:HOH103 4.9 7.1 0.3 C1' B:A11 4.9 19.3 1.0 O4' B:A11 4.9 22.2 1.0 O A:HOH60 5.0 44.1 1.0

M.C.Wahl, C.Ban, C.Sekharudu, B.Ramakrishnan, M.Sundaralingam. Structure of the Purine-Pyrimidine Alternating Rna Double Helix, R(Guauaua)D(C), with A 3'-Terminal Deoxy Residue. Acta Crystallogr.,Sect.D V. 52 655 1996.
ISSN: ISSN 0907-4449
PubMed: 15299629
DOI: 10.1107/S0907444996000248