Sodium in PDB 4rne: Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions

The structure of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions, PDB code: 4rne was solved by A.C.Fyfe, P.W.Dunten, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 1.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	37.656, 54.197, 95.677, 90.00, 90.00, 90.00
R / Rfree (%)	10.2 / 11.9

The structure of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions also contains other interesting chemical elements:

Strontium	(Sr)	7 atoms
Calcium	(Ca)	11 atoms

The binding sites of Sodium atom in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions (pdb code 4rne). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions, PDB code: 4rne:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:8.3 occ:0.85 NA B:NA302 0.0 8.3 0.8 NA B:NA302 1.4 6.5 0.1 O4 C:U306 2.6 11.2 1.0 O4 A:U106 2.6 9.3 0.6 O4 D:U406 2.7 12.9 1.0 O6 D:G405 2.7 8.6 1.0 O4 B:U206 2.8 10.8 1.0 O6 C:G305 2.8 8.0 1.0 O6 A:G105 2.8 7.8 1.0 O6 B:G205 2.9 7.2 1.0 O4 A:U106 3.1 7.1 0.4 H3 D:U406 3.2 9.2 1.0 SR B:SR301 3.2 12.9 1.0 H3 C:U306 3.2 9.6 1.0 H3 B:U206 3.4 10.0 1.0 H1 D:G405 3.5 9.0 1.0 H1 C:G305 3.5 11.3 1.0 C6 D:G405 3.5 8.9 1.0 H1 B:G205 3.5 9.7 1.0 C6 C:G305 3.6 7.8 1.0 C6 A:G105 3.6 8.3 1.0 C4 C:U306 3.6 10.6 1.0 C4 A:U106 3.6 9.1 0.6 C6 B:G205 3.6 7.0 1.0 C4 D:U406 3.7 12.9 1.0 C4 B:U206 3.8 10.1 1.0 N3 C:U306 3.8 11.4 1.0 NA B:NA303 3.8 21.0 0.5 N3 D:U406 3.9 13.1 1.0 N1 D:G405 3.9 9.3 1.0 N1 C:G305 3.9 7.8 1.0 N3 A:U106 3.9 8.8 0.6 N1 A:G105 3.9 7.9 1.0 N1 B:G205 4.0 7.5 1.0 N3 B:U206 4.0 10.8 1.0 C4 A:U106 4.0 7.0 0.4 N3 A:U106 4.2 8.1 0.4 C5 D:G405 4.7 9.8 1.0 C5 C:G305 4.7 7.9 1.0 C5 A:G105 4.7 8.3 1.0 C5 B:G205 4.8 7.3 1.0 C5 C:U306 4.9 11.5 1.0 C5 A:U106 5.0 9.6 0.6

Sodium binding site 2 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:6.5 occ:0.15 NA B:NA302 0.0 6.5 0.1 NA B:NA302 1.4 8.3 0.8 O4 A:U106 1.9 9.3 0.6 O4 B:U206 2.3 10.8 1.0 O4 A:U106 2.4 7.1 0.4 NA B:NA303 2.5 21.0 0.5 O4 D:U406 2.5 12.9 1.0 O4 C:U306 2.5 11.2 1.0 H3 B:U206 2.7 10.0 1.0 C4 A:U106 3.0 9.1 0.6 H3 C:U306 3.0 9.6 1.0 C4 B:U206 3.1 10.1 1.0 H3 D:U406 3.2 9.2 1.0 N3 B:U206 3.3 10.8 1.0 C4 A:U106 3.4 7.0 0.4 N3 A:U106 3.4 8.8 0.6 C4 C:U306 3.4 10.6 1.0 C4 D:U406 3.5 12.9 1.0 N3 C:U306 3.6 11.4 1.0 N3 A:U106 3.6 8.1 0.4 O6 A:G105 3.6 7.8 1.0 O6 B:G205 3.7 7.2 1.0 N3 D:U406 3.8 13.1 1.0 O6 D:G405 3.8 8.6 1.0 O6 C:G305 3.9 8.0 1.0 C6 A:G105 4.1 8.3 1.0 H1 D:G405 4.2 9.0 1.0 C5 A:U106 4.2 9.6 0.6 C6 B:G205 4.3 7.0 1.0 N1 A:G105 4.3 7.9 1.0 C6 D:G405 4.4 8.9 1.0 H1 B:G205 4.4 9.7 1.0 C5 B:U206 4.5 10.8 1.0 H1 C:G305 4.5 11.3 1.0 N1 D:G405 4.5 9.3 1.0 C6 C:G305 4.5 7.8 1.0 SR B:SR301 4.6 12.9 1.0 C2 B:U206 4.6 11.9 1.0 N1 B:G205 4.6 7.5 1.0 C5 A:U106 4.7 7.5 0.4 C2 A:U106 4.7 10.7 0.6 C5 C:U306 4.8 11.5 1.0 C5 D:U406 4.8 13.4 1.0 N1 C:G305 4.8 7.8 1.0 C2 C:U306 4.9 11.2 1.0 C2 A:U106 4.9 8.9 0.4 H5 B:U206 4.9 9.3 1.0 C5 A:G105 5.0 8.3 1.0

Sodium binding site 3 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:21.0 occ:0.47 NA B:NA302 2.5 6.5 0.1 O4 A:U106 3.0 9.3 0.6 O4 B:U206 3.1 10.8 1.0 H3 B:U206 3.3 10.0 1.0 O4 A:U106 3.3 7.1 0.4 C4 B:U206 3.4 10.1 1.0 N3 B:U206 3.5 10.8 1.0 C4 A:U106 3.5 9.1 0.6 O4 C:U306 3.6 11.2 1.0 H3 C:U306 3.7 9.6 1.0 O4 D:U406 3.7 12.9 1.0 C4 A:U106 3.8 7.0 0.4 NA B:NA302 3.8 8.3 0.8 N3 A:U106 4.0 8.8 0.6 N3 A:U106 4.1 8.1 0.4 C4 C:U306 4.1 10.6 1.0 N3 C:U306 4.1 11.4 1.0 H3 D:U406 4.2 9.2 1.0 C5 A:U106 4.3 9.6 0.6 C4 D:U406 4.3 12.9 1.0 C5 B:U206 4.4 10.8 1.0 C2 B:U206 4.4 11.9 1.0 N3 D:U406 4.6 13.1 1.0 C5 A:U106 4.7 7.5 0.4 H5 B:U206 4.8 9.3 1.0 O2 B:U206 4.9 14.2 1.0

Sodium binding site 4 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Na701 b:6.8 occ:0.23 NA F:NA701 0.0 6.8 0.2 NA F:NA701 0.9 20.8 0.3 O4 F:U606 2.7 12.2 0.7 O4 E:U506 2.8 11.9 0.7 O6 F:G605 2.9 9.5 1.0 O6 E:G505 2.9 9.8 1.0 O4 F:U606 3.0 21.0 0.3 H3 E:U506 3.3 12.6 0.7 SR E:SR601 3.4 11.5 0.5 H1 F:G605 3.6 17.2 1.0 H1 E:G505 3.6 19.5 1.0 C6 F:G605 3.6 9.8 1.0 C6 E:G505 3.6 10.0 1.0 N3 F:U606 3.7 19.1 0.3 C4 F:U606 3.7 12.0 0.7 C4 E:U506 3.7 10.8 0.7 C4 F:U606 3.8 19.6 0.3 N3 E:U506 3.9 11.6 0.7 N3 F:U606 3.9 12.4 0.7 N1 F:G605 3.9 9.8 1.0 N1 E:G505 4.0 9.8 1.0 C5 E:G505 4.7 10.3 1.0 C5 F:G605 4.7 10.6 1.0 C2 F:U606 4.9 19.2 0.3

Sodium binding site 5 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ F:Na701 b:20.8 occ:0.27 NA F:NA701 0.0 20.8 0.3 NA F:NA701 0.9 6.8 0.2 O4 F:U606 2.4 12.2 0.7 O4 E:U506 2.4 11.9 0.7 O4 F:U606 2.8 21.0 0.3 H3 E:U506 3.0 12.6 0.7 C4 F:U606 3.4 12.0 0.7 C4 E:U506 3.4 10.8 0.7 N3 F:U606 3.4 19.1 0.3 C4 F:U606 3.5 19.6 0.3 O6 E:G505 3.5 9.8 1.0 O6 F:G605 3.5 9.5 1.0 N3 E:U506 3.6 11.6 0.7 N3 F:U606 3.6 12.4 0.7 H1 F:G605 4.1 17.2 1.0 H1 E:G505 4.1 19.5 1.0 C6 F:G605 4.1 9.8 1.0 C6 E:G505 4.1 10.0 1.0 SR E:SR601 4.3 11.5 0.5 N1 F:G605 4.4 9.8 1.0 N1 E:G505 4.4 9.8 1.0 C2 F:U606 4.7 19.2 0.3 C5 F:U606 4.7 12.2 0.7 C5 E:U506 4.7 11.9 0.7 O G:HOH920 4.8 21.8 0.3 C5 F:U606 4.9 19.2 0.3 C2 E:U506 4.9 11.9 0.7 C2 F:U606 4.9 11.9 0.7

Sodium binding site 6 out of 6 in the Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ H:Na901 b:24.6 occ:0.50 O6 H:G805 2.4 12.4 1.0 O4 H:U806 2.6 21.9 0.7 O4 G:U706 2.8 28.4 0.8 O6 G:G705 3.0 11.8 1.0 SR G:SR802 3.1 12.0 0.5 C6 H:G805 3.2 11.2 1.0 H1 H:G805 3.5 15.8 1.0 C4 H:U806 3.5 31.2 0.7 N1 H:G805 3.7 11.8 1.0 C4 G:U706 3.8 28.3 0.8 N3 H:U806 3.9 34.2 0.7 C6 G:G705 3.9 12.0 1.0 N3 G:U706 4.0 31.8 0.8 H1 G:G705 4.0 21.0 1.0 O H:HOH1019 4.1 30.7 0.7 O H:HOH1017 4.1 22.3 0.6 C5 H:G805 4.3 12.6 1.0 N1 G:G705 4.4 12.9 1.0 O6 H:G804 4.7 9.6 1.0 N7 H:G805 4.8 12.8 1.0 C5 H:U806 4.8 27.3 0.7 C2 H:G805 5.0 11.7 1.0

A.C.Fyfe, P.W.Dunten, W.G.Scott. Structural Variations and Solvent Structure of Uggggu Quadruplexes Stabilized By SR2+ Ions To Be Published.