Sodium in PDB 1nta: 2.9 A Crystal Structure of Streptomycin Rna-Aptamer

The structure of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer, PDB code: 1nta was solved by V.Tereshko, E.Skripkin, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	83.097, 83.097, 49.472, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28.2

The structure of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer also contains other interesting chemical elements:

Barium

(Ba)

3 atoms

The binding sites of Sodium atom in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer (pdb code 1nta). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer, PDB code: 1nta:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na24 b:42.7 occ:1.00 OP2 A:U10 2.2 42.4 1.0 OP2 A:C7 2.2 48.1 1.0 C2' A:A8 3.4 62.1 1.0 P A:U10 3.5 43.4 1.0 P A:C7 3.6 51.0 1.0 C3' A:A8 3.8 60.9 1.0 O2' A:A8 3.9 64.4 1.0 OP1 A:U10 4.1 42.2 1.0 O3' A:G6 4.1 49.2 1.0 N3 B:C109 4.1 47.0 1.0 N4 B:C109 4.2 50.2 1.0 O5' A:U10 4.2 42.3 1.0 C5' A:U10 4.2 42.0 1.0 N2 A:G12 4.4 50.1 1.0 O4' A:U10 4.4 42.5 1.0 OP1 A:C7 4.4 50.9 1.0 C8 A:A8 4.5 66.7 1.0 O3' A:A8 4.5 59.8 1.0 C6 A:U10 4.6 43.1 1.0 O5' A:C7 4.7 52.9 1.0 C1' A:A8 4.7 63.7 1.0 C4 B:C109 4.7 47.9 1.0 O3' A:U9 4.7 44.4 1.0 C5 A:U10 4.9 44.4 1.0 C4' A:U10 4.9 41.2 1.0 C4' A:A8 4.9 60.8 1.0 O4' A:A8 5.0 62.4 1.0 N9 A:A8 5.0 66.1 1.0

Sodium binding site 2 out of 2 in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Na25 b:35.1 occ:0.50 OP2 A:C15 2.2 39.3 1.0 O4 A:U16 2.6 66.7 1.0 OP2 A:G12 3.3 41.8 1.0 C4 A:U16 3.3 67.0 1.0 P A:C15 3.5 42.2 1.0 C5 A:U16 3.7 66.2 1.0 OP1 A:C15 3.9 42.3 1.0 O5' A:A14 4.1 43.5 1.0 CH2 A:SRY26 4.1 36.7 1.0 N3 A:U16 4.4 67.5 1.0 P A:G12 4.5 41.3 1.0 OP2 A:A14 4.5 44.3 1.0 O3' A:A14 4.5 41.6 1.0 O5' A:C15 4.5 43.8 1.0 C3' A:A14 4.6 43.7 1.0 O5' A:G12 4.7 39.8 1.0 P A:A14 4.8 44.3 1.0 O51 A:SRY26 4.9 36.7 1.0 C6 A:U16 4.9 65.1 1.0

V.Tereshko, E.Skripkin, D.J.Patel. Encapsulating Streptomycin Within A Small 40-Mer Rna Chem.Biol. V. 10 175 2003.
ISSN: ISSN 1074-5521
PubMed: 12618190
DOI: 10.1016/S1074-5521(03)00024-3