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

The structure of 2.9 A Crystal Structure of Streptomycin Rna-Aptamer Complex, PDB code: 1ntb 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 (°)	82.634, 82.634, 49.153, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.5

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

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the 2.9 A Crystal Structure of Streptomycin Rna-Aptamer Complex (pdb code 1ntb). 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 Complex, PDB code: 1ntb:
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 Complex


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na23 b:52.0 occ:1.00 OP2 A:U10 2.5 50.0 1.0 OP2 A:C7 2.5 51.9 1.0 O2' A:A8 2.5 53.6 1.0 C2' A:A8 2.7 54.2 1.0 C3' A:A8 3.4 54.0 1.0 P A:U10 3.8 48.0 1.0 P A:C7 4.0 53.0 1.0 O3' A:U9 4.0 49.5 1.0 C1' A:A8 4.1 55.0 1.0 C8 A:A8 4.2 57.2 1.0 O3' A:A8 4.2 54.3 1.0 C5' A:U10 4.3 47.7 1.0 C4' A:A8 4.5 53.8 1.0 O5' A:U10 4.5 48.1 1.0 N9 A:A8 4.5 56.5 1.0 C3' A:U9 4.5 50.3 1.0 N2 A:G12 4.6 43.0 1.0 O4' A:A8 4.6 54.6 1.0 O5' A:C7 4.7 52.3 1.0 O3' A:G6 4.7 51.4 1.0 C5' A:A8 4.7 53.6 1.0 O4' A:U10 4.8 47.0 1.0 C4' A:U9 4.8 50.5 1.0 OP1 A:C7 4.9 53.0 1.0 N3 B:C109 4.9 46.0 1.0 OP1 A:U10 5.0 47.9 1.0 OP2 A:U9 5.0 52.3 1.0

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


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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na24 b:48.2 occ:1.00 O4 A:U16 2.2 50.2 1.0 OP2 A:C15 2.2 46.7 1.0 C4 A:U16 3.2 52.7 1.0 P A:C15 3.6 47.4 1.0 C5 A:U16 3.7 53.3 1.0 OP1 A:C15 4.1 47.2 1.0 OP2 A:G12 4.2 42.4 1.0 O5' A:A14 4.3 46.7 1.0 N3 A:U16 4.3 53.1 1.0 O3' A:A14 4.5 46.5 1.0 O5' A:C15 4.6 47.1 1.0 OP1 A:A14 4.7 46.6 1.0 C3' A:A14 4.7 46.4 1.0 OP2 A:A14 4.7 46.5 1.0 P A:A14 4.8 46.5 1.0 C42 A:SRY25 4.9 56.7 0.0

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