Sodium in PDB 2o4f: Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions

The structure of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions, PDB code: 2o4f was solved by C.Creze, B.Rinaldi, R.Haser, P.Bouvet, P.Gouet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.68 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.920, 57.370, 35.920, 90.00, 108.00, 90.00
R / Rfree (%)	20.4 / 25.7

The binding sites of Sodium atom in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions (pdb code 2o4f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions, PDB code: 2o4f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7 b:4.8 occ:1.00 O6 A:DG4 2.6 5.7 1.0 O6 D:DG34 2.6 6.8 1.0 O6 C:DG24 2.6 8.0 1.0 O6 B:DG14 2.6 5.5 1.0 O6 B:DG13 2.8 6.4 1.0 O6 A:DG3 3.0 5.2 1.0 O6 C:DG23 3.0 4.1 1.0 O6 D:DG33 3.2 6.3 1.0 C6 A:DG4 3.5 5.3 1.0 C6 D:DG34 3.5 4.9 1.0 C6 B:DG14 3.6 6.4 1.0 C6 B:DG13 3.6 3.4 1.0 C6 C:DG24 3.6 4.8 1.0 NA A:NA8 3.7 4.1 1.0 C6 C:DG23 3.7 3.9 1.0 C6 A:DG3 3.8 4.7 1.0 N1 A:DG4 3.8 4.0 1.0 N1 B:DG14 3.8 5.5 1.0 N1 D:DG34 3.8 6.3 1.0 C6 D:DG33 3.9 5.5 1.0 N1 B:DG13 3.9 2.7 1.0 N1 C:DG24 3.9 7.6 1.0 N1 C:DG23 3.9 4.5 1.0 N1 A:DG3 4.1 5.5 1.0 N1 D:DG33 4.1 4.2 1.0 NA A:NA10 4.6 6.7 1.0 C5 B:DG13 4.7 4.2 1.0 C5 A:DG4 4.8 6.1 1.0 C5 D:DG34 4.8 6.5 1.0 C5 C:DG24 4.8 6.9 1.0 C5 A:DG3 4.9 4.6 1.0 C5 B:DG14 4.9 5.7 1.0 C5 C:DG23 4.9 3.6 1.0 C5 D:DG33 5.0 6.8 1.0

Sodium binding site 2 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8 b:4.1 occ:1.00 O6 C:DG22 2.8 5.8 1.0 O6 A:DG3 2.8 5.2 1.0 O6 C:DG23 2.8 4.1 1.0 O6 B:DG13 2.8 6.4 1.0 O6 A:DG2 2.8 3.2 1.0 O6 D:DG33 2.9 6.3 1.0 O6 B:DG12 2.9 2.8 1.0 O6 D:DG32 2.9 4.9 1.0 NA A:NA9 3.5 3.5 1.0 C6 C:DG22 3.6 6.9 1.0 C6 A:DG2 3.6 5.4 1.0 C6 D:DG32 3.7 5.9 1.0 C6 B:DG12 3.7 6.2 1.0 C6 C:DG23 3.7 3.9 1.0 NA A:NA7 3.7 4.8 1.0 C6 B:DG13 3.7 3.4 1.0 C6 A:DG3 3.7 4.7 1.0 C6 D:DG33 3.8 5.5 1.0 N1 C:DG22 3.9 3.7 1.0 N1 B:DG12 3.9 5.3 1.0 N1 C:DG23 4.0 4.5 1.0 N1 D:DG32 4.0 4.8 1.0 N1 A:DG2 4.0 3.2 1.0 N1 B:DG13 4.0 2.7 1.0 N1 A:DG3 4.0 5.5 1.0 N1 D:DG33 4.1 4.2 1.0 C5 C:DG22 4.8 6.2 1.0 C5 A:DG2 4.8 4.2 1.0 C5 D:DG32 4.8 3.8 1.0 C5 B:DG12 4.8 5.3 1.0 C5 B:DG13 4.9 4.2 1.0 C5 C:DG23 5.0 3.6 1.0 C5 A:DG3 5.0 4.6 1.0

Sodium binding site 3 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9 b:3.5 occ:1.00 O6 F:DG52 2.7 6.0 1.0 O6 A:DG2 2.7 3.2 1.0 O6 H:DG72 2.8 3.3 1.0 O6 G:DG62 2.8 1.2 1.0 O6 B:DG12 2.8 2.8 1.0 O6 E:DG42 2.8 5.3 1.0 O6 D:DG32 2.8 4.9 1.0 O6 C:DG22 2.8 5.8 1.0 NA E:NA3 3.4 3.2 1.0 NA A:NA8 3.5 4.1 1.0 C6 H:DG72 3.6 4.3 1.0 C6 G:DG62 3.6 2.5 1.0 C6 E:DG42 3.6 5.5 1.0 C6 F:DG52 3.6 3.9 1.0 C6 B:DG12 3.7 6.2 1.0 C6 A:DG2 3.7 5.4 1.0 C6 C:DG22 3.7 6.9 1.0 C6 D:DG32 3.8 5.9 1.0 N1 H:DG72 3.9 2.5 1.0 N1 E:DG42 3.9 6.8 1.0 N1 G:DG62 4.0 1.4 1.0 N1 F:DG52 4.0 2.0 1.0 N1 B:DG12 4.0 5.3 1.0 N1 C:DG22 4.1 3.7 1.0 N1 A:DG2 4.1 3.2 1.0 N1 D:DG32 4.1 4.8 1.0 C5 H:DG72 4.7 5.1 1.0 C5 G:DG62 4.8 4.0 1.0 C5 F:DG52 4.8 5.1 1.0 C5 E:DG42 4.8 5.8 1.0 C5 B:DG12 4.9 5.3 1.0 C5 A:DG2 5.0 4.2 1.0 C5 C:DG22 5.0 6.2 1.0

Sodium binding site 4 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na10 b:6.7 occ:1.00 O6 A:DG5 2.2 7.3 1.0 O6 B:DG15 2.2 5.1 1.0 O6 D:DG35 2.3 7.5 1.0 O6 C:DG25 2.3 6.4 1.0 O A:HOH20 2.4 6.7 1.0 C6 B:DG15 3.2 4.6 1.0 C6 A:DG5 3.2 6.0 1.0 C6 D:DG35 3.3 8.5 1.0 C6 C:DG25 3.3 4.4 1.0 N1 C:DG25 3.6 6.7 1.0 N1 A:DG5 3.6 6.8 1.0 N1 D:DG35 3.6 6.8 1.0 N1 B:DG15 3.6 3.5 1.0 O6 D:DG34 4.0 6.8 1.0 O6 C:DG24 4.0 8.0 1.0 O6 B:DG14 4.1 5.5 1.0 O6 A:DG4 4.2 5.7 1.0 O4 A:DT6 4.4 7.2 1.0 C6 C:DG24 4.5 4.8 1.0 C6 D:DG34 4.5 4.9 1.0 C6 B:DG14 4.5 6.4 1.0 C5 A:DG5 4.6 6.7 1.0 C5 B:DG15 4.6 4.7 1.0 C5 C:DG25 4.6 3.7 1.0 C5 D:DG35 4.6 5.5 1.0 NA A:NA7 4.6 4.8 1.0 C6 A:DG4 4.7 5.3 1.0 N1 D:DG34 4.8 6.3 1.0 N1 B:DG14 4.8 5.5 1.0 N1 C:DG24 4.8 7.6 1.0 N1 A:DG4 4.9 4.0 1.0 C2 C:DG25 4.9 6.5 1.0 C2 A:DG5 4.9 5.7 1.0 C2 D:DG35 5.0 8.3 1.0 C2 B:DG15 5.0 4.8 1.0

Sodium binding site 5 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Na3 b:3.2 occ:1.00 O6 F:DG53 2.6 4.4 1.0 O6 G:DG63 2.6 4.1 1.0 O6 H:DG73 2.6 6.3 1.0 O6 E:DG43 2.6 4.2 1.0 O6 H:DG72 2.6 3.3 1.0 O6 G:DG62 2.7 1.2 1.0 O6 F:DG52 2.8 6.0 1.0 O6 E:DG42 2.8 5.3 1.0 NA A:NA9 3.4 3.5 1.0 NA E:NA4 3.5 3.9 1.0 C6 E:DG43 3.5 4.0 1.0 C6 G:DG63 3.6 5.4 1.0 C6 H:DG72 3.6 4.3 1.0 C6 F:DG53 3.6 5.3 1.0 C6 H:DG73 3.6 6.0 1.0 C6 G:DG62 3.6 2.5 1.0 C6 F:DG52 3.7 3.9 1.0 C6 E:DG42 3.7 5.5 1.0 N1 E:DG43 3.9 4.8 1.0 N1 H:DG72 3.9 2.5 1.0 N1 F:DG53 3.9 5.4 1.0 N1 G:DG63 3.9 3.9 1.0 N1 H:DG73 3.9 3.8 1.0 N1 G:DG62 4.0 1.4 1.0 N1 E:DG42 4.0 6.8 1.0 N1 F:DG52 4.0 2.0 1.0 C5 H:DG72 4.8 5.1 1.0 C5 G:DG62 4.8 4.0 1.0 C5 E:DG43 4.8 2.8 1.0 C5 G:DG63 4.8 4.5 1.0 C5 H:DG73 4.8 5.3 1.0 C5 F:DG53 4.9 6.3 1.0 C5 E:DG42 4.9 5.8 1.0 C5 F:DG52 4.9 5.1 1.0 O6 E:DG44 5.0 7.2 1.0

Sodium binding site 6 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Na4 b:3.9 occ:1.00 O6 E:DG44 2.4 7.2 1.0 O6 F:DG54 2.5 4.4 1.0 O6 H:DG74 2.6 3.7 1.0 O6 G:DG64 2.7 5.2 1.0 O6 H:DG73 2.9 6.3 1.0 O6 G:DG63 3.0 4.1 1.0 O6 E:DG43 3.1 4.2 1.0 O6 F:DG53 3.1 4.4 1.0 C6 E:DG44 3.4 7.0 1.0 NA E:NA3 3.5 3.2 1.0 C6 F:DG54 3.5 5.2 1.0 C6 H:DG74 3.6 5.1 1.0 C6 H:DG73 3.6 6.0 1.0 C6 G:DG64 3.7 5.5 1.0 C6 G:DG63 3.7 5.4 1.0 N1 E:DG44 3.8 7.6 1.0 N1 F:DG54 3.8 5.4 1.0 C6 E:DG43 3.8 4.0 1.0 C6 F:DG53 3.9 5.3 1.0 N1 H:DG73 3.9 3.8 1.0 N1 H:DG74 4.0 5.8 1.0 N1 G:DG64 4.0 4.7 1.0 N1 G:DG63 4.1 3.9 1.0 N1 E:DG43 4.1 4.8 1.0 N1 F:DG53 4.2 5.4 1.0 NA E:NA6 4.7 12.1 1.0 C5 H:DG73 4.7 5.3 1.0 C5 E:DG44 4.8 7.1 1.0 C5 G:DG63 4.8 4.5 1.0 C5 F:DG54 4.9 4.3 1.0 C5 H:DG74 4.9 8.3 1.0 C5 E:DG43 5.0 2.8 1.0 C5 G:DG64 5.0 5.4 1.0 C5 F:DG53 5.0 6.3 1.0

Sodium binding site 7 out of 7 in the Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Parallel-Stranded Guanine Tetraplex Crystallised with Monovalent Ions within 5.0Å range: probe atom residue distance (Å) B Occ E:Na6 b:12.1 occ:1.00 O6 H:DG75 2.2 7.6 1.0 O6 F:DG55 2.2 7.2 1.0 O6 E:DG45 2.3 6.1 1.0 O6 G:DG65 2.3 7.7 1.0 C6 F:DG55 3.2 6.7 1.0 C6 H:DG75 3.3 7.6 1.0 C6 G:DG65 3.3 5.9 1.0 C6 E:DG45 3.3 5.7 1.0 N1 G:DG65 3.6 6.3 1.0 N1 F:DG55 3.6 8.6 1.0 N1 E:DG45 3.6 5.2 1.0 N1 H:DG75 3.6 6.5 1.0 O6 H:DG74 3.8 3.7 1.0 O6 E:DG44 4.2 7.2 1.0 O6 G:DG64 4.2 5.2 1.0 O4 F:DT56 4.3 23.3 1.0 O6 F:DG54 4.3 4.4 1.0 C6 H:DG74 4.4 5.1 1.0 C6 E:DG44 4.5 7.0 1.0 C5 F:DG55 4.5 8.8 1.0 C5 G:DG65 4.6 5.3 1.0 C5 H:DG75 4.6 7.2 1.0 N1 E:DG44 4.6 7.6 1.0 C5 E:DG45 4.6 6.1 1.0 NA E:NA4 4.7 3.9 1.0 N1 H:DG74 4.7 5.8 1.0 C6 F:DG54 4.7 5.2 1.0 O4 E:DT46 4.7 7.4 1.0 C6 G:DG64 4.8 5.5 1.0 N1 F:DG54 4.9 5.4 1.0 C2 G:DG65 4.9 6.6 1.0 C2 F:DG55 5.0 7.6 1.0 C2 E:DG45 5.0 6.6 1.0 C2 H:DG75 5.0 7.5 1.0

C.Creze, B.Rinaldi, R.Haser, P.Bouvet, P.Gouet. Structure of A D(Tggggt) Quadruplex Crystallized in the Presence of Li+ Ions. Acta Crystallogr.,Sect.D V. 63 682 2007.
ISSN: ISSN 0907-4449
PubMed: 17505106
DOI: 10.1107/S0907444907013315