Potassium in PDB 1i0o: 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt

The structure of 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt, PDB code: 1i0o 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 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.650, 44.610, 44.160, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.6

The binding sites of Potassium atom in the 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt (pdb code 1i0o). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt, PDB code: 1i0o:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:K21 b:31.1 occ:1.00 OP1 A:DC10 2.7 25.3 1.0 O3' A:DG9 2.8 23.8 1.0 P A:DC10 3.4 24.6 1.0 C3' A:DG9 4.1 24.4 1.0 C5' A:DC10 4.3 23.0 1.0 O5' A:DC10 4.3 24.8 1.0 C4' A:DG9 4.4 24.3 1.0 OP2 A:DC10 4.6 25.5 1.0 C2' A:DG9 4.8 23.7 1.0 O A:HOH157 4.9 59.5 1.0 C5' A:DG9 4.9 24.6 1.0

Potassium binding site 2 out of 3 in the 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt within 5.0Å range: probe atom residue distance (Å) B Occ A:K22 b:35.2 occ:1.00 O A:HOH146 2.7 35.9 1.0 O4 A:DT4 2.8 24.6 1.0 O A:HOH151 3.2 44.7 1.0 O6 A:DG3 3.3 21.5 1.0 O A:HOH161 3.4 43.7 1.0 N7 A:DG3 3.6 22.4 1.0 N6 A:DA5 3.7 20.1 1.0 C6 A:DG3 3.7 22.0 1.0 C7 A:DT4 3.8 23.5 1.0 C4 A:DT4 3.8 23.5 1.0 C5 A:DG3 3.8 23.0 1.0 N6 B:DA17 4.1 25.4 1.0 O A:HOH152 4.2 46.8 1.0 C5 A:DT4 4.3 23.9 1.0 O B:HOH187 4.4 51.2 1.0 O4 B:T2316 4.5 26.3 1.0 C8 A:DG3 4.6 22.9 1.0 C6 A:DA5 4.7 21.8 1.0 N6 B:DA15 4.8 21.5 1.0 N1 A:DG3 4.8 20.4 1.0 N7 A:DA5 4.9 22.2 1.0 C4 A:DG3 4.9 23.1 1.0

Potassium binding site 3 out of 3 in the 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of 1.6 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-3'-Methylenephosphonate Thymine in Place of T6, High K-Salt within 5.0Å range: probe atom residue distance (Å) B Occ B:K23 b:35.0 occ:1.00 O3' B:DC20 2.5 26.2 1.0 C3' B:DC20 3.4 25.3 1.0 C4' B:DC20 3.6 26.3 1.0 C2' B:DC20 4.0 25.7 1.0 O B:HOH125 4.0 57.9 1.0 C5' B:DC20 4.4 26.4 1.0 O4' B:DC20 4.6 25.1 1.0 C1' B:DC20 4.9 25.1 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