Sodium in PDB 352d: The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution

The structure of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution, PDB code: 352d was solved by K.Phillips, Z.Dauter, A.I.H.Murchie, D.M.J.Lilley, B.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 0.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.280, 34.780, 56.230, 74.31, 77.68, 89.81
R / Rfree (%)	15.2 / n/a

The structure of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution also contains other interesting chemical elements:

Calcium

(Ca)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution (pdb code 352d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution, PDB code: 352d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na159 b:4.6 occ:1.00 O6 B:DG13 2.6 5.0 1.0 O6 D:DG33 2.6 5.2 1.0 O6 A:DG3 2.6 5.1 1.0 O6 C:DG23 2.7 6.0 1.0 O6 C:DG22 2.8 4.8 1.0 O6 D:DG32 2.9 4.7 1.0 O6 B:DG12 2.9 4.8 1.0 O6 A:DG2 3.0 5.1 1.0 NA A:NA160 3.5 4.5 1.0 C6 B:DG13 3.5 4.7 1.0 C6 D:DG33 3.6 5.0 1.0 C6 A:DG3 3.6 4.8 1.0 C6 C:DG22 3.6 4.2 1.0 C6 C:DG23 3.6 5.6 1.0 C6 D:DG32 3.7 4.2 1.0 C6 B:DG12 3.7 4.5 1.0 NA B:NA164 3.7 7.5 1.0 C6 A:DG2 3.8 3.9 1.0 N1 B:DG13 3.8 5.0 1.0 N1 A:DG3 3.9 4.6 1.0 N1 D:DG33 3.9 5.3 1.0 N1 C:DG23 3.9 5.0 1.0 N1 C:DG22 3.9 4.5 1.0 N1 D:DG32 4.0 4.1 1.0 N1 B:DG12 4.0 3.8 1.0 N1 A:DG2 4.1 4.4 1.0 C5 C:DG22 4.7 4.7 1.0 C5 B:DG13 4.8 4.8 1.0 C5 D:DG32 4.8 4.8 1.0 C5 D:DG33 4.8 5.4 1.0 C5 B:DG12 4.8 4.4 1.0 C5 A:DG3 4.9 5.1 1.0 O6 B:DG14 4.9 7.8 1.0 C5 A:DG2 4.9 4.4 1.0 O6 A:DG4 4.9 6.6 1.0 C5 C:DG23 4.9 5.6 1.0

Sodium binding site 2 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na160 b:4.5 occ:1.00 O6 A:DG2 2.7 5.1 1.0 O6 D:DG32 2.7 4.7 1.0 O6 B:DG12 2.7 4.8 1.0 O6 H:DG72 2.7 5.8 1.0 O6 E:DG42 2.7 5.1 1.0 O6 C:DG22 2.7 4.8 1.0 O6 G:DG62 2.7 5.8 1.0 O6 F:DG52 2.8 4.9 1.0 NA G:NA161 3.4 5.3 1.0 NA A:NA159 3.5 4.6 1.0 C6 E:DG42 3.6 5.1 1.0 C6 H:DG72 3.6 5.5 1.0 C6 D:DG32 3.6 4.2 1.0 C6 B:DG12 3.6 4.5 1.0 C6 F:DG52 3.6 4.6 1.0 C6 A:DG2 3.6 3.9 1.0 C6 G:DG62 3.6 5.8 1.0 C6 C:DG22 3.6 4.2 1.0 N1 E:DG42 3.9 4.8 1.0 N1 G:DG62 3.9 4.8 1.0 N1 H:DG72 3.9 6.2 1.0 N1 F:DG52 3.9 4.5 1.0 N1 B:DG12 3.9 3.8 1.0 N1 C:DG22 3.9 4.5 1.0 N1 A:DG2 3.9 4.4 1.0 N1 D:DG32 4.0 4.1 1.0 C5 E:DG42 4.8 4.6 1.0 C5 H:DG72 4.8 6.1 1.0 C5 F:DG52 4.8 4.9 1.0 C5 D:DG32 4.8 4.8 1.0 C5 G:DG62 4.8 6.0 1.0 C5 B:DG12 4.9 4.4 1.0 C5 C:DG22 4.9 4.7 1.0 C5 A:DG2 4.9 4.4 1.0

Sodium binding site 3 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na170 b:7.8 occ:1.00 O6 C:DG25 2.3 7.3 1.0 O6 D:DG35 2.3 7.1 1.0 O6 B:DG15 2.3 8.2 1.0 O6 A:DG5 2.3 7.6 1.0 C6 C:DG25 3.3 8.1 1.0 C6 B:DG15 3.3 8.5 1.0 C6 A:DG5 3.3 7.4 1.0 C6 D:DG35 3.3 6.8 1.0 N1 C:DG25 3.6 8.5 1.0 N1 B:DG15 3.6 7.8 1.0 N1 A:DG5 3.6 6.8 1.0 N1 D:DG35 3.7 8.2 1.0 O6 C:DG24 3.9 7.0 1.0 O6 B:DG14 3.9 7.8 1.0 O6 D:DG34 4.1 6.3 1.0 NA B:NA164 4.2 7.5 1.0 C6 C:DG24 4.3 7.8 1.0 O6 A:DG4 4.3 6.6 1.0 O4 A:DT6 4.4 8.4 1.0 C6 B:DG14 4.4 7.5 1.0 N1 C:DG24 4.5 7.5 1.0 C6 D:DG34 4.6 5.9 1.0 C5 B:DG15 4.6 8.4 1.0 C5 C:DG25 4.6 8.9 1.0 C5 D:DG35 4.6 7.3 1.0 C5 A:DG5 4.7 7.5 1.0 N1 B:DG14 4.7 7.5 1.0 N1 D:DG34 4.8 6.5 1.0 C6 A:DG4 4.9 6.3 1.0 C2 C:DG25 4.9 9.0 1.0 C2 B:DG15 4.9 8.4 1.0 C2 A:DG5 5.0 6.9 1.0 C2 D:DG35 5.0 8.1 1.0

Sodium binding site 4 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na164 b:7.5 occ:1.00 O6 B:DG14 2.3 7.8 1.0 O6 D:DG34 2.4 6.3 1.0 O6 C:DG24 2.4 7.0 1.0 O6 A:DG4 2.4 6.6 1.0 O6 C:DG23 3.0 6.0 1.0 O6 D:DG33 3.2 5.2 1.0 C6 D:DG34 3.4 5.9 1.0 C6 B:DG14 3.4 7.5 1.0 O6 B:DG13 3.4 5.0 1.0 C6 A:DG4 3.4 6.3 1.0 C6 C:DG24 3.4 7.8 1.0 O6 A:DG3 3.6 5.1 1.0 N1 D:DG34 3.7 6.5 1.0 N1 B:DG14 3.7 7.5 1.0 N1 A:DG4 3.7 6.1 1.0 NA A:NA159 3.7 4.6 1.0 C6 C:DG23 3.8 5.6 1.0 N1 C:DG24 3.8 7.5 1.0 C6 D:DG33 3.8 5.0 1.0 N1 D:DG33 4.0 5.3 1.0 C6 B:DG13 4.1 4.7 1.0 N1 C:DG23 4.1 5.0 1.0 NA A:NA170 4.2 7.8 1.0 C6 A:DG3 4.3 4.8 1.0 N1 B:DG13 4.4 5.0 1.0 N1 A:DG3 4.5 4.6 1.0 O6 A:DG5 4.5 7.6 1.0 C5 D:DG34 4.7 6.3 1.0 C5 B:DG14 4.7 8.4 1.0 C5 A:DG4 4.7 6.4 1.0 C5 C:DG24 4.7 8.9 1.0 O6 D:DG35 4.8 7.1 1.0 O6 B:DG15 4.8 8.2 1.0 C5 C:DG23 4.8 5.6 1.0 C5 D:DG33 4.9 5.4 1.0 O6 C:DG25 4.9 7.3 1.0

Sodium binding site 5 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na165 b:7.9 occ:1.00 O6 H:DG74 2.4 8.5 1.0 O6 F:DG54 2.4 7.4 1.0 O6 E:DG44 2.4 7.2 1.0 O6 G:DG64 2.4 7.7 1.0 O6 G:DG63 3.2 5.9 1.0 O6 H:DG73 3.2 6.5 1.0 O6 F:DG53 3.2 5.7 1.0 O6 E:DG43 3.3 5.7 1.0 C6 H:DG74 3.4 8.9 1.0 C6 F:DG54 3.4 7.0 1.0 C6 E:DG44 3.4 7.4 1.0 C6 G:DG64 3.5 7.4 1.0 NA G:NA161 3.6 5.3 1.0 N1 E:DG44 3.7 7.6 1.0 N1 H:DG74 3.7 9.1 1.0 N1 F:DG54 3.7 6.5 1.0 N1 G:DG64 3.8 6.5 1.0 C6 G:DG63 3.9 5.4 1.0 C6 H:DG73 3.9 5.5 1.0 C6 F:DG53 4.0 5.0 1.0 C6 E:DG43 4.0 6.0 1.0 N1 H:DG73 4.2 6.7 1.0 N1 G:DG63 4.2 5.7 1.0 NA E:NA169 4.2 7.4 1.0 N1 E:DG43 4.3 5.9 1.0 N1 F:DG53 4.3 5.0 1.0 C5 H:DG74 4.7 10.9 1.0 C5 F:DG54 4.7 6.4 1.0 O6 H:DG75 4.7 8.7 1.0 C5 E:DG44 4.7 8.4 1.0 O6 E:DG45 4.7 7.8 1.0 C5 G:DG64 4.8 8.2 1.0 O6 G:DG65 4.8 7.1 1.0 O6 F:DG55 4.9 7.5 1.0 C5 G:DG63 4.9 6.0 1.0 C5 H:DG73 4.9 6.6 1.0

Sodium binding site 6 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na169 b:7.4 occ:1.00 O6 E:DG45 2.3 7.8 1.0 O6 F:DG55 2.3 7.5 1.0 O6 G:DG65 2.3 7.1 1.0 O6 H:DG75 2.3 8.7 1.0 C6 E:DG45 3.3 8.3 1.0 C6 G:DG65 3.3 7.6 1.0 C6 H:DG75 3.3 7.9 1.0 C6 F:DG55 3.3 7.1 1.0 N1 G:DG65 3.6 7.3 1.0 N1 E:DG45 3.6 8.0 1.0 N1 H:DG75 3.6 7.7 1.0 N1 F:DG55 3.7 6.6 1.0 O6 F:DG54 4.0 7.4 1.0 O6 H:DG74 4.1 8.5 1.0 O6 E:DG44 4.1 7.2 1.0 O6 G:DG64 4.1 7.7 1.0 NA E:NA165 4.2 7.9 1.0 O4 G:DT66 4.5 7.5 1.0 C6 F:DG54 4.5 7.0 1.0 C6 H:DG74 4.6 8.9 1.0 C6 E:DG44 4.6 7.4 1.0 C5 E:DG45 4.6 8.4 1.0 C6 G:DG64 4.6 7.4 1.0 C5 H:DG75 4.6 8.9 1.0 C5 G:DG65 4.6 7.0 1.0 C5 F:DG55 4.6 7.3 1.0 N1 F:DG54 4.8 6.5 1.0 N1 E:DG44 4.8 7.6 1.0 N1 H:DG74 4.8 9.1 1.0 N1 G:DG64 4.8 6.5 1.0 C2 E:DG45 4.9 9.4 1.0 C2 G:DG65 4.9 7.2 1.0 C2 H:DG75 5.0 9.4 1.0

Sodium binding site 7 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ G:Na161 b:5.3 occ:1.00 O6 E:DG43 2.5 5.7 1.0 O6 G:DG63 2.5 5.9 1.0 O6 F:DG53 2.5 5.7 1.0 O6 H:DG73 2.5 6.5 1.0 O6 E:DG42 2.7 5.1 1.0 O6 F:DG52 2.7 4.9 1.0 O6 G:DG62 2.8 5.8 1.0 O6 H:DG72 2.9 5.8 1.0 NA A:NA160 3.4 4.5 1.0 C6 G:DG63 3.5 5.4 1.0 C6 E:DG43 3.5 6.0 1.0 C6 H:DG73 3.5 5.5 1.0 C6 F:DG53 3.5 5.0 1.0 NA E:NA165 3.6 7.9 1.0 C6 E:DG42 3.6 5.1 1.0 C6 F:DG52 3.6 4.6 1.0 C6 G:DG62 3.7 5.8 1.0 C6 H:DG72 3.7 5.5 1.0 N1 G:DG63 3.8 5.7 1.0 N1 E:DG43 3.8 5.9 1.0 N1 H:DG73 3.9 6.7 1.0 N1 F:DG53 3.9 5.0 1.0 N1 F:DG52 3.9 4.5 1.0 N1 E:DG42 4.0 4.8 1.0 N1 G:DG62 4.0 4.8 1.0 N1 H:DG72 4.1 6.2 1.0 C5 G:DG63 4.8 6.0 1.0 C5 E:DG42 4.8 4.6 1.0 C5 E:DG43 4.8 5.3 1.0 C5 F:DG53 4.8 5.4 1.0 C5 H:DG73 4.8 6.6 1.0 C5 F:DG52 4.8 4.9 1.0 C5 G:DG62 4.9 6.0 1.0 O6 E:DG44 4.9 7.2 1.0 C5 H:DG72 4.9 6.1 1.0 O6 F:DG54 4.9 7.4 1.0 O6 G:DG64 5.0 7.7 1.0 O6 H:DG74 5.0 8.5 1.0

Sodium binding site 8 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Na158 b:4.5 occ:1.00 O6 O:DG142 2.7 5.0 1.0 O6 M:DG122 2.7 4.7 1.0 O6 N:DG132 2.7 5.3 1.0 O6 P:DG152 2.7 4.9 1.0 O6 L:DG112 2.7 5.6 1.0 O6 I:DG82 2.7 5.1 1.0 O6 J:DG92 2.7 5.5 1.0 O6 K:DG102 2.8 5.8 1.0 NA K:NA162 3.4 5.9 1.0 NA M:NA157 3.5 4.7 1.0 C6 I:DG82 3.6 4.9 1.0 C6 O:DG142 3.6 4.9 1.0 C6 L:DG112 3.6 4.9 1.0 C6 J:DG92 3.6 5.2 1.0 C6 M:DG122 3.6 4.2 1.0 C6 K:DG102 3.6 5.5 1.0 C6 N:DG132 3.7 4.5 1.0 C6 P:DG152 3.7 4.7 1.0 N1 I:DG82 3.9 4.5 1.0 N1 O:DG142 3.9 4.0 1.0 N1 L:DG112 3.9 5.1 1.0 N1 J:DG92 3.9 5.2 1.0 N1 K:DG102 3.9 5.8 1.0 N1 M:DG122 3.9 4.0 1.0 N1 P:DG152 3.9 4.5 1.0 N1 N:DG132 4.0 4.7 1.0 C5 I:DG82 4.8 4.8 1.0 C5 L:DG112 4.8 5.5 1.0 C5 J:DG92 4.8 5.4 1.0 C5 O:DG142 4.8 4.6 1.0 C5 K:DG102 4.9 6.3 1.0 C5 M:DG122 4.9 4.4 1.0 C5 N:DG132 4.9 4.7 1.0 C5 P:DG152 4.9 4.5 1.0

Sodium binding site 9 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Na166 b:7.1 occ:1.00 O6 J:DG95 2.3 7.4 1.0 O6 I:DG85 2.3 7.3 1.0 O6 K:DG105 2.3 7.4 1.0 O6 L:DG115 2.3 7.9 1.0 C6 K:DG105 3.3 7.2 1.0 C6 J:DG95 3.3 6.9 1.0 C6 I:DG85 3.3 7.1 1.0 C6 L:DG115 3.3 7.4 1.0 N1 K:DG105 3.6 7.1 1.0 N1 J:DG95 3.6 7.2 1.0 N1 I:DG85 3.6 7.3 1.0 N1 L:DG115 3.6 7.8 1.0 O6 L:DG114 4.1 7.6 1.0 O6 K:DG104 4.1 6.5 1.0 O6 J:DG94 4.1 7.2 1.0 O6 I:DG84 4.2 7.2 1.0 NA I:NA167 4.3 7.6 1.0 O4 I:DT86 4.4 7.2 1.0 C6 L:DG114 4.5 8.1 1.0 C5 J:DG95 4.6 7.3 1.0 C5 K:DG105 4.6 7.1 1.0 C6 K:DG104 4.6 7.2 1.0 C6 J:DG94 4.6 7.2 1.0 C5 I:DG85 4.6 7.2 1.0 C5 L:DG115 4.6 8.5 1.0 C6 I:DG84 4.7 7.6 1.0 N1 L:DG114 4.8 7.5 1.0 N1 K:DG104 4.8 6.7 1.0 N1 J:DG94 4.9 6.7 1.0 C2 K:DG105 4.9 6.9 1.0 N1 I:DG84 4.9 7.0 1.0 C2 J:DG95 4.9 7.8 1.0 C2 I:DG85 5.0 7.7 1.0 C2 L:DG115 5.0 7.9 1.0

Sodium binding site 10 out of 14 in the The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Crystal Structure of A Parallel-Stranded Parallel- Stranded Guanine Tetraplex at 0.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Na167 b:7.6 occ:1.00 O6 L:DG114 2.4 7.6 1.0 O6 J:DG94 2.4 7.2 1.0 O6 K:DG104 2.4 6.5 1.0 O6 I:DG84 2.4 7.2 1.0 O6 K:DG103 3.2 6.6 1.0 O6 J:DG93 3.2 6.1 1.0 O6 I:DG83 3.3 5.9 1.0 O6 L:DG113 3.3 6.3 1.0 C6 L:DG114 3.4 8.1 1.0 C6 J:DG94 3.4 7.2 1.0 C6 I:DG84 3.4 7.6 1.0 C6 K:DG104 3.4 7.2 1.0 NA K:NA162 3.6 5.9 1.0 N1 J:DG94 3.7 6.7 1.0 N1 L:DG114 3.7 7.5 1.0 N1 I:DG84 3.7 7.0 1.0 N1 K:DG104 3.8 6.7 1.0 C6 K:DG103 3.9 6.2 1.0 C6 J:DG93 3.9 5.5 1.0 C6 L:DG113 4.0 5.9 1.0 C6 I:DG83 4.0 5.5 1.0 N1 K:DG103 4.2 5.6 1.0 N1 J:DG93 4.3 5.5 1.0 N1 L:DG113 4.3 6.2 1.0 NA I:NA166 4.3 7.1 1.0 N1 I:DG83 4.3 5.6 1.0 O6 J:DG95 4.7 7.4 1.0 C5 L:DG114 4.7 8.3 1.0 C5 J:DG94 4.7 7.0 1.0 C5 K:DG104 4.7 7.5 1.0 C5 I:DG84 4.7 7.0 1.0 O6 I:DG85 4.8 7.3 1.0 O6 K:DG105 4.8 7.4 1.0 O6 L:DG115 4.9 7.9 1.0 C5 J:DG93 4.9 6.0 1.0 C5 K:DG103 5.0 6.7 1.0

K.Phillips, Z.Dauter, A.I.Murchie, D.M.Lilley, B.Luisi. The Crystal Structure of A Parallel-Stranded Guanine Tetraplex at 0.95 A Resolution. J.Mol.Biol. V. 273 171 1997.
ISSN: ISSN 0022-2836
PubMed: 9367755
DOI: 10.1006/JMBI.1997.1292