Sodium in PDB 1i0q: 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt

The structure of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt, PDB code: 1i0q was solved by V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.130, 44.530, 45.130, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19

The binding sites of Sodium atom in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt (pdb code 1i0q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt, PDB code: 1i0q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na22 b:21.6 occ:1.00 O4 A:DT4 2.6 9.3 1.0 O A:HOH124 3.1 20.6 1.0 N6 A:DA5 3.4 8.9 1.0 O6 A:DG3 3.5 11.6 1.0 O A:HOH139 3.5 25.4 1.0 C7 A:DT4 3.6 10.6 1.0 C4 A:DT4 3.6 9.3 1.0 O A:HOH122 3.6 25.2 1.0 C6 A:DG3 3.7 10.3 1.0 N7 A:DG3 3.8 10.6 1.0 C5 A:DG3 3.9 9.2 1.0 N6 B:DA17 4.0 10.1 1.0 C5 A:DT4 4.1 9.6 1.0 C6 A:DA5 4.4 9.2 1.0 N7 A:DA5 4.5 9.0 1.0 O4 B:12616 4.5 10.4 1.0 O A:HOH177 4.6 26.7 1.0 C8 A:DG3 4.7 9.0 1.0 N1 A:DG3 4.7 9.2 1.0 C5 A:DA5 4.8 8.4 1.0 N3 A:DT4 4.8 7.7 1.0 C4 A:DG3 4.9 9.9 1.0 N6 B:DA15 5.0 10.7 1.0

Sodium binding site 2 out of 2 in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Na-Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:Na23 b:25.3 occ:1.00 O A:HOH110 2.6 12.5 1.0 OP1 A:DC10 2.8 17.3 1.0 P A:DC10 3.5 15.1 1.0 OP2 A:DC10 3.6 16.1 1.0 O5' A:DC10 3.9 11.3 1.0 C5' A:DC10 4.6 12.4 1.0 O A:HOH149 4.6 26.6 1.0 O3' A:DC10 4.9 11.2 1.0 O A:HOH165 5.0 34.5 1.0

V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli. Detection of Alkali Metal Ions in Dna Crystals Using State-of-the-Art X-Ray Diffraction Experiments. Nucleic Acids Res. V. 29 1208 2001.
ISSN: ISSN 0305-1048
PubMed: 11222771
DOI: 10.1093/NAR/29.5.1208