Sodium in PDB 244d: The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex

The structure of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d was solved by G.Laughlan, A.I.H.Murchie, D.G.Norman, M.H.Moore, P.C.E.Moody, 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)	8.00 / 1.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.760, 35.470, 56.770, 74.39, 77.64, 89.73
R / Rfree (%)	12.4 / 17.6

The structure of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex 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 High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex (pdb code 244d). 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 High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d:
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 High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na159 b:4.9 occ:1.00 O6 B:DG13 2.6 7.2 1.0 O6 D:DG33 2.7 7.6 1.0 O6 A:DG3 2.7 7.5 1.0 O6 C:DG23 2.7 7.5 1.0 O6 C:DG22 2.9 6.6 1.0 O6 B:DG12 2.9 6.8 1.0 O6 D:DG32 3.0 6.3 1.0 O6 A:DG2 3.0 6.9 1.0 NA A:NA160 3.5 5.1 1.0 C6 B:DG13 3.6 5.6 1.0 C6 A:DG3 3.7 6.0 1.0 C6 D:DG33 3.7 6.8 1.0 C6 C:DG23 3.7 6.8 1.0 C6 C:DG22 3.7 5.5 1.0 C6 D:DG32 3.7 5.3 1.0 C6 B:DG12 3.7 5.5 1.0 C6 A:DG2 3.8 5.7 1.0 NA B:NA164 3.8 9.4 1.0 N1 A:DG3 3.9 6.1 1.0 N1 B:DG13 4.0 6.1 1.0 N1 D:DG33 4.0 7.2 1.0 N1 C:DG23 4.0 6.6 1.0 N1 D:DG32 4.0 5.8 1.0 N1 B:DG12 4.1 5.7 1.0 N1 C:DG22 4.1 5.5 1.0 N1 A:DG2 4.1 5.6 1.0 C5 C:DG22 4.8 5.2 1.0 C5 B:DG12 4.8 6.4 1.0 C5 D:DG32 4.9 6.0 1.0 C5 A:DG2 4.9 5.9 1.0 C5 B:DG13 4.9 6.1 1.0 C5 D:DG33 4.9 6.5 1.0 C5 A:DG3 5.0 6.1 1.0 C5 C:DG23 5.0 7.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na160 b:5.1 occ:1.00 O6 D:DG32 2.7 6.3 1.0 O6 A:DG2 2.7 6.9 1.0 O6 B:DG12 2.7 6.8 1.0 O6 C:DG22 2.7 6.6 1.0 O6 F:DG52 2.7 6.2 1.0 O6 E:DG42 2.7 6.2 1.0 O6 H:DG72 2.8 8.0 1.0 O6 G:DG62 2.8 7.0 1.0 NA E:NA161 3.4 7.6 1.0 NA A:NA159 3.5 4.9 1.0 C6 H:DG72 3.6 7.3 1.0 C6 E:DG42 3.6 6.1 1.0 C6 F:DG52 3.6 6.0 1.0 C6 D:DG32 3.6 5.3 1.0 C6 G:DG62 3.7 7.3 1.0 C6 A:DG2 3.7 5.7 1.0 C6 B:DG12 3.7 5.5 1.0 C6 C:DG22 3.7 5.5 1.0 N1 E:DG42 3.9 6.7 1.0 N1 H:DG72 3.9 7.3 1.0 N1 G:DG62 4.0 7.3 1.0 N1 F:DG52 4.0 5.8 1.0 N1 D:DG32 4.0 5.8 1.0 N1 B:DG12 4.0 5.7 1.0 N1 A:DG2 4.0 5.6 1.0 N1 C:DG22 4.0 5.5 1.0 C5 H:DG72 4.8 7.3 1.0 C5 E:DG42 4.8 6.0 1.0 C5 F:DG52 4.9 6.0 1.0 C5 G:DG62 4.9 7.8 1.0 C5 D:DG32 4.9 6.0 1.0 C5 B:DG12 4.9 6.4 1.0 C5 A:DG2 4.9 5.9 1.0 C5 C:DG22 4.9 5.2 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na170 b:10.5 occ:1.00 O6 A:DG5 2.3 9.4 1.0 O6 B:DG15 2.3 10.0 1.0 O6 D:DG35 2.4 9.8 1.0 O6 C:DG25 2.4 10.7 1.0 O A:HOH205 2.4 12.7 1.0 C6 B:DG15 3.3 11.8 1.0 C6 C:DG25 3.3 10.6 1.0 C6 A:DG5 3.3 9.0 1.0 C6 D:DG35 3.4 9.5 1.0 N1 C:DG25 3.6 10.4 1.0 N1 A:DG5 3.6 9.0 1.0 N1 B:DG15 3.7 10.5 1.0 N1 D:DG35 3.7 9.0 1.0 O6 C:DG24 3.9 9.8 1.0 O6 B:DG14 4.1 8.9 1.0 O6 D:DG34 4.1 8.1 1.0 O6 A:DG4 4.3 8.1 1.0 NA B:NA164 4.3 9.4 1.0 C6 C:DG24 4.4 9.8 1.0 C6 B:DG14 4.5 8.7 1.0 O4 A:DT6 4.6 11.0 1.0 N1 C:DG24 4.6 9.7 1.0 C5 B:DG15 4.6 11.4 1.0 C5 C:DG25 4.6 11.0 1.0 C6 D:DG34 4.7 7.7 1.0 C5 A:DG5 4.7 8.3 1.0 C5 D:DG35 4.7 9.1 1.0 N1 D:DG34 4.8 7.8 1.0 N1 B:DG14 4.8 8.6 1.0 C6 A:DG4 4.9 7.1 1.0 C2 C:DG25 5.0 10.7 1.0 C2 A:DG5 5.0 9.1 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na164 b:9.4 occ:1.00 O6 B:DG14 2.4 8.9 1.0 O6 D:DG34 2.4 8.1 1.0 O6 A:DG4 2.5 8.1 1.0 O6 C:DG24 2.5 9.8 1.0 O6 C:DG23 3.1 7.5 1.0 O6 D:DG33 3.3 7.6 1.0 O6 B:DG13 3.3 7.2 1.0 C6 D:DG34 3.4 7.7 1.0 C6 A:DG4 3.4 7.1 1.0 C6 B:DG14 3.4 8.7 1.0 C6 C:DG24 3.5 9.8 1.0 O6 A:DG3 3.5 7.5 1.0 N1 D:DG34 3.7 7.8 1.0 N1 B:DG14 3.8 8.6 1.0 N1 A:DG4 3.8 7.7 1.0 NA A:NA159 3.8 4.9 1.0 C6 C:DG23 3.8 6.8 1.0 N1 C:DG24 3.8 9.7 1.0 C6 D:DG33 4.0 6.8 1.0 C6 B:DG13 4.0 5.6 1.0 N1 D:DG33 4.1 7.2 1.0 N1 C:DG23 4.2 6.6 1.0 C6 A:DG3 4.3 6.0 1.0 NA A:NA170 4.3 10.5 1.0 N1 B:DG13 4.4 6.1 1.0 N1 A:DG3 4.5 6.1 1.0 O6 A:DG5 4.7 9.4 1.0 C5 D:DG34 4.7 7.5 1.0 C5 B:DG14 4.7 9.3 1.0 C5 A:DG4 4.8 7.4 1.0 C5 C:DG24 4.8 10.0 1.0 O6 B:DG15 4.8 10.0 1.0 C5 C:DG23 4.9 7.4 1.0 O6 D:DG35 4.9 9.8 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na161 b:7.6 occ:1.00 O6 E:DG43 2.5 8.2 1.0 O6 H:DG73 2.5 8.4 1.0 O6 F:DG53 2.5 7.1 1.0 O6 G:DG63 2.6 7.4 1.0 O6 E:DG42 2.8 6.2 1.0 O6 F:DG52 2.8 6.2 1.0 O6 G:DG62 2.9 7.0 1.0 O6 H:DG72 2.9 8.0 1.0 NA A:NA160 3.4 5.1 1.0 C6 E:DG43 3.5 7.5 1.0 C6 H:DG73 3.5 7.3 1.0 C6 G:DG63 3.6 7.9 1.0 C6 F:DG53 3.6 6.4 1.0 NA E:NA165 3.7 10.0 1.0 C6 E:DG42 3.7 6.1 1.0 C6 F:DG52 3.7 6.0 1.0 C6 H:DG72 3.8 7.3 1.0 C6 G:DG62 3.8 7.3 1.0 N1 E:DG43 3.9 6.7 1.0 N1 F:DG53 3.9 6.4 1.0 N1 G:DG63 3.9 7.0 1.0 N1 H:DG73 3.9 7.7 1.0 N1 F:DG52 4.0 5.8 1.0 N1 E:DG42 4.0 6.7 1.0 N1 G:DG62 4.0 7.3 1.0 N1 H:DG72 4.1 7.3 1.0 C5 E:DG43 4.8 6.9 1.0 C5 H:DG73 4.8 8.2 1.0 C5 F:DG53 4.8 6.4 1.0 C5 G:DG63 4.8 7.8 1.0 C5 E:DG42 4.9 6.0 1.0 C5 F:DG52 4.9 6.0 1.0 C5 H:DG72 5.0 7.3 1.0 C5 G:DG62 5.0 7.8 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na165 b:10.0 occ:1.00 O6 F:DG54 2.4 8.3 1.0 O6 E:DG44 2.4 8.9 1.0 O6 H:DG74 2.5 10.7 1.0 O6 G:DG64 2.5 9.0 1.0 O6 F:DG53 3.2 7.1 1.0 O6 G:DG63 3.3 7.4 1.0 O6 E:DG43 3.3 8.2 1.0 O6 H:DG73 3.3 8.4 1.0 C6 F:DG54 3.4 8.0 1.0 C6 E:DG44 3.5 8.8 1.0 C6 H:DG74 3.5 10.7 1.0 C6 G:DG64 3.5 9.8 1.0 NA E:NA161 3.7 7.6 1.0 N1 F:DG54 3.8 7.7 1.0 N1 H:DG74 3.8 10.2 1.0 N1 G:DG64 3.8 8.7 1.0 N1 E:DG44 3.8 10.2 1.0 C6 H:DG73 4.0 7.3 1.0 C6 E:DG43 4.0 7.5 1.0 C6 G:DG63 4.0 7.9 1.0 C6 F:DG53 4.0 6.4 1.0 N1 E:DG43 4.2 6.7 1.0 N1 H:DG73 4.3 7.7 1.0 N1 F:DG53 4.3 6.4 1.0 N1 G:DG63 4.3 7.0 1.0 NA E:NA169 4.4 10.0 1.0 C5 F:DG54 4.7 8.3 1.0 C5 E:DG44 4.7 9.6 1.0 C5 H:DG74 4.8 10.9 1.0 C5 G:DG64 4.8 8.7 1.0 O6 H:DG75 4.8 11.2 1.0 O6 E:DG45 4.9 9.6 1.0 O6 G:DG65 4.9 9.4 1.0 O6 F:DG55 5.0 9.7 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Na169 b:10.0 occ:1.00 O6 H:DG75 2.3 11.2 1.0 O6 G:DG65 2.3 9.4 1.0 O6 F:DG55 2.3 9.7 1.0 O6 E:DG45 2.4 9.6 1.0 O G:HOH194 2.4 9.7 1.0 C6 E:DG45 3.3 10.3 1.0 C6 H:DG75 3.3 10.9 1.0 C6 G:DG65 3.4 9.0 1.0 C6 F:DG55 3.4 9.8 1.0 N1 E:DG45 3.6 9.6 1.0 N1 H:DG75 3.6 10.8 1.0 N1 G:DG65 3.7 8.6 1.0 N1 F:DG55 3.7 8.9 1.0 O6 F:DG54 4.1 8.3 1.0 O6 E:DG44 4.1 8.9 1.0 O6 H:DG74 4.2 10.7 1.0 O6 G:DG64 4.2 9.0 1.0 NA E:NA165 4.4 10.0 1.0 C6 F:DG54 4.6 8.0 1.0 O4 G:DT66 4.6 11.6 1.0 C6 E:DG44 4.6 8.8 1.0 C6 H:DG74 4.6 10.7 1.0 C5 H:DG75 4.7 10.9 1.0 C5 E:DG45 4.7 10.3 1.0 C5 G:DG65 4.7 9.5 1.0 C5 F:DG55 4.7 8.5 1.0 C6 G:DG64 4.7 9.8 1.0 N1 F:DG54 4.8 7.7 1.0 N1 E:DG44 4.9 10.2 1.0 N1 H:DG74 4.9 10.2 1.0 N1 G:DG64 4.9 8.7 1.0 C2 H:DG75 5.0 11.2 1.0 C2 E:DG45 5.0 10.7 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ I:Na158 b:4.4 occ:1.00 O6 N:DG132 2.7 7.0 1.0 O6 M:DG122 2.7 6.8 1.0 O6 O:DG142 2.7 6.8 1.0 O6 P:DG152 2.7 6.7 1.0 O6 L:DG112 2.7 6.9 1.0 O6 I:DG82 2.8 6.8 1.0 O6 J:DG92 2.8 7.3 1.0 O6 K:DG102 2.8 7.3 1.0 NA L:NA162 3.5 7.5 1.0 NA M:NA157 3.5 4.7 1.0 C6 L:DG112 3.6 6.3 1.0 C6 J:DG92 3.6 6.2 1.0 C6 I:DG82 3.6 5.7 1.0 C6 K:DG102 3.7 6.2 1.0 C6 N:DG132 3.7 5.7 1.0 C6 M:DG122 3.7 5.5 1.0 C6 O:DG142 3.7 5.7 1.0 C6 P:DG152 3.7 5.5 1.0 N1 L:DG112 3.9 6.2 1.0 N1 J:DG92 3.9 6.7 1.0 N1 I:DG82 3.9 6.1 1.0 N1 K:DG102 4.0 7.1 1.0 N1 O:DG142 4.0 6.3 1.0 N1 M:DG122 4.0 5.8 1.0 N1 N:DG132 4.0 5.6 1.0 N1 P:DG152 4.0 5.1 1.0 C5 J:DG92 4.8 6.6 1.0 C5 L:DG112 4.8 7.1 1.0 C5 I:DG82 4.8 5.7 1.0 C5 K:DG102 4.9 6.7 1.0 C5 O:DG142 4.9 6.5 1.0 C5 M:DG122 4.9 5.2 1.0 C5 N:DG132 5.0 5.6 1.0 C5 P:DG152 5.0 5.7 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ I:Na166 b:10.0 occ:1.00 O6 I:DG85 2.3 9.6 1.0 O6 L:DG115 2.3 10.6 1.0 O6 J:DG95 2.3 9.3 1.0 O6 K:DG105 2.4 10.1 1.0 O I:HOH200 2.4 10.0 1.0 C6 I:DG85 3.3 9.7 1.0 C6 J:DG95 3.3 8.7 1.0 C6 K:DG105 3.3 10.3 1.0 C6 L:DG115 3.4 10.2 1.0 N1 K:DG105 3.6 9.9 1.0 N1 J:DG95 3.6 9.5 1.0 N1 I:DG85 3.6 10.0 1.0 N1 L:DG115 3.7 10.0 1.0 O6 L:DG114 4.1 9.3 1.0 O6 K:DG104 4.2 8.9 1.0 O6 J:DG94 4.2 9.2 1.0 O6 I:DG84 4.3 9.7 1.0 NA I:NA167 4.4 10.3 1.0 O4 I:DT86 4.5 11.0 1.0 C6 L:DG114 4.6 8.7 1.0 C5 I:DG85 4.6 9.3 1.0 C5 J:DG95 4.6 9.8 1.0 C6 K:DG104 4.7 9.7 1.0 C5 K:DG105 4.7 11.3 1.0 C5 L:DG115 4.7 10.2 1.0 C6 J:DG94 4.7 8.0 1.0 C6 I:DG84 4.8 9.4 1.0 N1 K:DG104 4.9 9.7 1.0 N1 L:DG114 4.9 9.1 1.0 N1 J:DG94 4.9 8.6 1.0 C2 K:DG105 4.9 10.8 1.0 C2 J:DG95 5.0 9.9 1.0 C2 I:DG85 5.0 9.4 1.0 N1 I:DG84 5.0 8.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range: probe atom residue distance (Å) B Occ I:Na167 b:10.3 occ:1.00 O6 K:DG104 2.4 8.9 1.0 O6 J:DG94 2.4 9.2 1.0 O6 L:DG114 2.5 9.3 1.0 O6 I:DG84 2.5 9.7 1.0 O6 J:DG93 3.2 7.8 1.0 O6 K:DG103 3.3 7.6 1.0 O6 I:DG83 3.3 7.7 1.0 O6 L:DG113 3.4 7.8 1.0 C6 J:DG94 3.4 8.0 1.0 C6 K:DG104 3.4 9.7 1.0 C6 L:DG114 3.4 8.7 1.0 C6 I:DG84 3.5 9.4 1.0 NA L:NA162 3.7 7.5 1.0 N1 J:DG94 3.8 8.6 1.0 N1 K:DG104 3.8 9.7 1.0 N1 L:DG114 3.8 9.1 1.0 N1 I:DG84 3.8 8.9 1.0 C6 J:DG93 3.9 6.9 1.0 C6 K:DG103 4.0 8.5 1.0 C6 I:DG83 4.0 6.2 1.0 C6 L:DG113 4.1 7.1 1.0 N1 J:DG93 4.2 6.4 1.0 N1 K:DG103 4.3 7.7 1.0 N1 L:DG113 4.4 6.9 1.0 N1 I:DG83 4.4 6.8 1.0 NA I:NA166 4.4 10.0 1.0 C5 J:DG94 4.7 8.7 1.0 C5 K:DG104 4.7 9.6 1.0 C5 L:DG114 4.8 8.9 1.0 C5 I:DG84 4.8 8.8 1.0 O6 J:DG95 4.8 9.3 1.0 O6 I:DG85 4.9 9.6 1.0 O6 K:DG105 4.9 10.1 1.0 C5 J:DG93 4.9 7.8 1.0

G.Laughlan, A.I.Murchie, D.G.Norman, M.H.Moore, P.C.Moody, D.M.Lilley, B.Luisi. The High-Resolution Crystal Structure of A Parallel-Stranded Guanine Tetraplex. Science V. 265 520 1994.
ISSN: ISSN 0036-8075
PubMed: 8036494