Sodium in PDB 1o0k: Structure of the First Parallel Dna Quadruplex-Drug Complex

The structure of Structure of the First Parallel Dna Quadruplex-Drug Complex, PDB code: 1o0k was solved by G.R.Clark, P.D.Pytel, C.J.Squire, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.004, 47.073, 31.865, 90.00, 119.80, 90.00
R / Rfree (%)	n/a / 20.6

The binding sites of Sodium atom in the Structure of the First Parallel Dna Quadruplex-Drug Complex (pdb code 1o0k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the First Parallel Dna Quadruplex-Drug Complex, PDB code: 1o0k:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of the First Parallel Dna Quadruplex-Drug Complex


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 First Parallel Dna Quadruplex-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na28 b:5.8 occ:1.00 O6 D:DG1023 2.5 12.2 1.0 O6 B:DG1011 2.5 13.0 1.0 O6 A:DG1005 2.5 12.4 1.0 O6 C:DG1017 2.5 11.9 1.0 O6 B:DG1010 3.0 10.2 1.0 O6 A:DG1004 3.1 10.1 1.0 O6 C:DG1016 3.1 10.6 1.0 O6 D:DG1022 3.2 10.2 1.0 C6 B:DG1011 3.5 12.5 1.0 C6 D:DG1023 3.5 12.6 1.0 C6 A:DG1005 3.5 13.0 1.0 C6 C:DG1017 3.5 11.4 1.0 NA C:NA29 3.7 2.8 1.0 C6 B:DG1010 3.7 9.6 1.0 N1 A:DG1005 3.8 13.4 1.0 N1 D:DG1023 3.8 13.4 1.0 N1 B:DG1011 3.8 13.8 1.0 N1 C:DG1017 3.8 11.9 1.0 C6 A:DG1004 3.8 9.4 1.0 C6 C:DG1016 3.8 10.2 1.0 C6 D:DG1022 3.9 10.0 1.0 N1 B:DG1010 4.0 10.1 1.0 N1 C:DG1016 4.1 10.2 1.0 N1 A:DG1004 4.2 10.5 1.0 N1 D:DG1022 4.2 9.7 1.0 O B:HOH1231 4.6 50.0 1.0 O A:HOH1234 4.7 50.0 1.0 C5 B:DG1011 4.8 14.4 1.0 C5 B:DG1010 4.8 10.1 1.0 C5 D:DG1023 4.8 12.3 1.0 C5 A:DG1005 4.8 15.9 1.0 C5 C:DG1017 4.8 11.9 1.0 C5 A:DG1004 4.9 10.8 1.0 C5 C:DG1016 5.0 10.4 1.0

Sodium binding site 2 out of 3 in the Structure of the First Parallel Dna Quadruplex-Drug Complex


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 First Parallel Dna Quadruplex-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na30 b:2.9 occ:1.00 O6 B:DG1008 2.4 8.6 1.0 O6 D:DG1020 2.4 8.4 1.0 O6 C:DG1014 2.5 8.5 1.0 O6 A:DG1002 2.5 9.2 1.0 O6 D:DG1021 2.9 9.0 1.0 O6 C:DG1015 2.9 8.4 1.0 O6 A:DG1003 3.1 8.8 1.0 O6 B:DG1009 3.2 9.4 1.0 C6 D:DG1020 3.4 8.2 1.0 C6 B:DG1008 3.4 8.7 1.0 C6 C:DG1014 3.4 8.9 1.0 C6 A:DG1002 3.4 8.3 1.0 NA C:NA29 3.6 2.8 1.0 C6 D:DG1021 3.7 8.4 1.0 C6 C:DG1015 3.7 8.9 1.0 N1 D:DG1020 3.7 8.7 1.0 N1 B:DG1008 3.7 8.7 1.0 N1 C:DG1014 3.7 8.5 1.0 N1 A:DG1002 3.8 8.1 1.0 C6 A:DG1003 3.9 8.3 1.0 N1 D:DG1021 4.0 8.6 1.0 C6 B:DG1009 4.1 9.5 1.0 N1 C:DG1015 4.1 8.7 1.0 N1 A:DG1003 4.1 8.8 1.0 N1 B:DG1009 4.4 9.4 1.0 O19 D:DM126 4.6 8.5 1.0 C5 C:DG1014 4.7 9.2 1.0 C1 D:DM126 4.7 7.7 1.0 C5 A:DG1002 4.7 9.6 1.0 C5 B:DG1008 4.7 9.2 1.0 C5 D:DG1020 4.7 8.8 1.0 C5 C:DG1015 4.8 8.6 1.0 C5 D:DG1021 4.9 8.8 1.0

Sodium binding site 3 out of 3 in the Structure of the First Parallel Dna Quadruplex-Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the First Parallel Dna Quadruplex-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na29 b:2.8 occ:1.00 O6 C:DG1015 2.6 8.4 1.0 O6 D:DG1022 2.6 10.2 1.0 O6 B:DG1010 2.6 10.2 1.0 O6 A:DG1003 2.6 8.8 1.0 O6 A:DG1004 2.7 10.1 1.0 O6 C:DG1016 2.7 10.6 1.0 O6 B:DG1009 2.7 9.4 1.0 O6 D:DG1021 2.9 9.0 1.0 C6 C:DG1015 3.5 8.9 1.0 C6 A:DG1003 3.5 8.3 1.0 C6 B:DG1010 3.6 9.6 1.0 C6 D:DG1022 3.6 10.0 1.0 C6 B:DG1009 3.6 9.5 1.0 C6 A:DG1004 3.6 9.4 1.0 NA A:NA30 3.6 2.9 1.0 C6 C:DG1016 3.6 10.2 1.0 NA A:NA28 3.7 5.8 1.0 C6 D:DG1021 3.7 8.4 1.0 N1 C:DG1015 3.8 8.7 1.0 N1 A:DG1003 3.9 8.8 1.0 N1 B:DG1009 3.9 9.4 1.0 N1 B:DG1010 3.9 10.1 1.0 N1 D:DG1022 3.9 9.7 1.0 N1 C:DG1016 4.0 10.2 1.0 N1 A:DG1004 4.0 10.5 1.0 N1 D:DG1021 4.0 8.6 1.0 C5 C:DG1015 4.7 8.6 1.0 C5 A:DG1003 4.7 8.5 1.0 C5 B:DG1009 4.8 8.8 1.0 C5 B:DG1010 4.8 10.1 1.0 C5 D:DG1022 4.9 10.4 1.0 C5 D:DG1021 4.9 8.8 1.0 C5 A:DG1004 4.9 10.8 1.0 C5 C:DG1016 4.9 10.4 1.0 O6 B:DG1008 5.0 8.6 1.0

G.R.Clark, P.D.Pytel, C.J.Squire, S.Neidle. Structure of the First Parallel Dna Quadruplex-Drug Complex J.Am.Chem.Soc. V. 125 4066 2003.
ISSN: ISSN 0002-7863
PubMed: 12670225
DOI: 10.1021/JA0297988