Sodium in PDB 2gw0: A D(Tggggt)- Sodium and Calcium Complex.

The structure of A D(Tggggt)- Sodium and Calcium Complex., PDB code: 2gw0 was solved by M.P.H.Lee, G.N.Parkinson, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.357, 27.911, 34.969, 89.11, 75.63, 79.70
R / Rfree (%)	17.4 / 22.4

The structure of A D(Tggggt)- Sodium and Calcium Complex. also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Sodium atom in the A D(Tggggt)- Sodium and Calcium Complex. (pdb code 2gw0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the A D(Tggggt)- Sodium and Calcium Complex., PDB code: 2gw0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na49 b:13.6 occ:1.00 O6 D:DG23 2.3 11.7 1.0 O6 B:DG11 2.3 7.9 1.0 O6 A:DG5 2.3 11.1 1.0 O6 C:DG17 2.3 11.5 1.0 O B:HOH61 2.5 10.3 1.0 C6 D:DG23 3.3 9.6 1.0 C6 B:DG11 3.3 9.3 1.0 C6 A:DG5 3.3 11.9 1.0 C6 C:DG17 3.4 11.4 1.0 N1 B:DG11 3.6 11.0 1.0 N1 D:DG23 3.6 11.4 1.0 N1 A:DG5 3.7 11.7 1.0 N1 C:DG17 3.7 12.2 1.0 O6 A:DG4 3.8 9.9 1.0 O6 D:DG22 3.8 10.4 1.0 O6 C:DG16 3.9 10.4 1.0 O6 B:DG10 4.1 8.0 1.0 C6 D:DG22 4.3 9.3 1.0 CA D:CA53 4.4 19.4 1.0 C6 A:DG4 4.4 6.6 1.0 C6 C:DG16 4.5 9.5 1.0 N1 D:DG22 4.6 14.4 1.0 C5 D:DG23 4.6 10.3 1.0 N1 A:DG4 4.6 8.7 1.0 C5 B:DG11 4.6 10.4 1.0 C5 A:DG5 4.7 11.4 1.0 C5 C:DG17 4.7 19.5 1.0 O4 B:DT12 4.7 16.2 1.0 C6 B:DG10 4.7 10.3 1.0 N1 C:DG16 4.8 10.7 1.0 N1 B:DG10 4.9 9.4 1.0 C2 B:DG11 5.0 6.4 1.0 C2 D:DG23 5.0 9.8 1.0

Sodium binding site 2 out of 4 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na51 b:12.5 occ:1.00 O6 H:DG46 2.4 14.9 1.0 O6 E:DG28 2.4 10.4 1.0 O6 G:DG40 2.5 11.6 1.0 O6 F:DG34 2.6 10.3 1.0 O6 F:DG33 3.0 12.9 1.0 O6 H:DG45 3.1 7.8 1.0 O6 G:DG39 3.1 10.9 1.0 O6 E:DG27 3.2 9.0 1.0 C6 H:DG46 3.4 11.6 1.0 C6 E:DG28 3.4 10.5 1.0 NA F:NA50 3.5 9.6 1.0 C6 G:DG40 3.5 8.8 1.0 C6 F:DG34 3.6 8.2 1.0 N1 H:DG46 3.7 12.3 1.0 N1 E:DG28 3.7 10.3 1.0 C6 F:DG33 3.7 6.2 1.0 C6 H:DG45 3.8 11.5 1.0 C6 G:DG39 3.9 11.0 1.0 N1 G:DG40 3.9 12.5 1.0 N1 F:DG34 3.9 13.4 1.0 C6 E:DG27 3.9 6.6 1.0 N1 F:DG33 4.1 10.2 1.0 N1 H:DG45 4.1 7.0 1.0 N1 G:DG39 4.2 11.3 1.0 N1 E:DG27 4.3 8.4 1.0 NA E:NA52 4.3 15.2 1.0 C5 H:DG46 4.7 11.0 1.0 C5 E:DG28 4.8 9.2 1.0 C5 G:DG40 4.8 10.7 1.0 C5 F:DG33 4.9 7.5 1.0 C5 H:DG45 4.9 8.8 1.0 O6 E:DG29 4.9 8.9 1.0 C5 F:DG34 4.9 11.7 1.0 O6 F:DG35 4.9 11.2 1.0 O6 G:DG41 4.9 12.3 1.0 C5 G:DG39 4.9 14.3 1.0

Sodium binding site 3 out of 4 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range: probe atom residue distance (Å) B Occ E:Na52 b:15.2 occ:1.00 O6 H:DG47 2.3 12.2 1.0 O6 E:DG29 2.3 8.9 1.0 O6 F:DG35 2.3 11.2 1.0 O6 G:DG41 2.3 12.3 1.0 O E:HOH62 2.4 13.7 1.0 C6 H:DG47 3.3 9.5 1.0 C6 E:DG29 3.3 7.6 1.0 C6 G:DG41 3.3 6.1 1.0 C6 F:DG35 3.3 7.0 1.0 N1 E:DG29 3.6 11.2 1.0 N1 G:DG41 3.6 9.6 1.0 N1 H:DG47 3.6 11.5 1.0 N1 F:DG35 3.7 13.6 1.0 O6 H:DG46 3.9 14.9 1.0 O6 F:DG34 3.9 10.3 1.0 O6 G:DG40 4.0 11.6 1.0 O6 E:DG28 4.1 10.4 1.0 NA E:NA51 4.3 12.5 1.0 C6 H:DG46 4.4 11.6 1.0 C6 G:DG40 4.5 8.8 1.0 C6 F:DG34 4.5 8.2 1.0 O4 E:DT30 4.6 10.0 1.0 C5 H:DG47 4.6 10.4 1.0 C5 E:DG29 4.6 14.1 1.0 C6 E:DG28 4.6 10.5 1.0 C5 G:DG41 4.6 6.2 1.0 C5 F:DG35 4.7 10.5 1.0 N1 H:DG46 4.7 12.3 1.0 N1 G:DG40 4.8 12.5 1.0 N1 F:DG34 4.8 13.4 1.0 N1 E:DG28 4.9 10.3 1.0 C2 G:DG41 4.9 9.9 1.0 C2 E:DG29 4.9 8.2 1.0 C2 H:DG47 5.0 11.0 1.0

Sodium binding site 4 out of 4 in the A D(Tggggt)- Sodium and Calcium Complex.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A D(Tggggt)- Sodium and Calcium Complex. within 5.0Å range: probe atom residue distance (Å) B Occ F:Na50 b:9.6 occ:1.00 O6 F:DG33 2.5 12.9 1.0 O6 E:DG27 2.6 9.0 1.0 O6 H:DG45 2.6 7.8 1.0 O6 G:DG39 2.6 10.9 1.0 O6 E:DG26 2.7 7.6 1.0 O6 F:DG32 2.7 8.9 1.0 O6 H:DG44 2.8 11.0 1.0 O6 G:DG38 2.8 11.3 1.0 CA A:CA55 3.3 14.4 1.0 C6 F:DG33 3.4 6.2 1.0 NA E:NA51 3.5 12.5 1.0 C6 E:DG26 3.6 6.6 1.0 C6 E:DG27 3.6 6.6 1.0 C6 G:DG39 3.6 11.0 1.0 C6 H:DG45 3.6 11.5 1.0 C6 F:DG32 3.6 9.5 1.0 C6 H:DG44 3.7 9.8 1.0 C6 G:DG38 3.7 14.1 1.0 N1 F:DG33 3.8 10.2 1.0 N1 E:DG26 3.9 6.0 1.0 N1 G:DG39 3.9 11.3 1.0 N1 F:DG32 3.9 6.8 1.0 N1 H:DG45 3.9 7.0 1.0 N1 E:DG27 3.9 8.4 1.0 N1 H:DG44 4.0 5.8 1.0 N1 G:DG38 4.1 8.0 1.0 C5 F:DG33 4.7 7.5 1.0 C5 E:DG26 4.8 10.9 1.0 C5 E:DG27 4.8 9.2 1.0 C5 G:DG39 4.8 14.3 1.0 C5 H:DG45 4.9 8.8 1.0 C5 F:DG32 4.9 11.6 1.0 O6 E:DG28 4.9 10.4 1.0 C5 H:DG44 5.0 10.6 1.0 C5 G:DG38 5.0 11.2 1.0

M.P.Lee, G.N.Parkinson, P.Hazel, S.Neidle. Observation of the Coexistence of Sodium and Calcium Ions in A Dna G-Quadruplex Ion Channel. J.Am.Chem.Soc. V. 129 10106 2007.
ISSN: ISSN 0002-7863
PubMed: 17661470
DOI: 10.1021/JA0740869