Sodium in PDB 4rkv: 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: 4rkv 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)	37.08 / 0.88
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	36.645, 36.645, 37.078, 90.00, 90.00, 90.00
R / Rfree (%)	9.3 / 9.8

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

Strontium	(Sr)	6 atoms
Calcium	(Ca)	2 atoms

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

Sodium binding site 1 out of 4 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 A:Na9003 b:9.9 occ:0.08 O B:HOH2225 3.5 44.0 1.0 NA B:NA2103 4.0 8.9 0.1

Sodium binding site 2 out of 4 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 A:Na9003 b:8.2 occ:0.17 O4 A:U1006 2.3 8.9 1.0 H3 A:U1006 3.0 10.8 1.0 C4 A:U1006 3.2 8.6 1.0 N3 A:U1006 3.5 9.4 1.0 O6 A:G1005 3.9 7.9 1.0 C6 A:G1005 4.4 7.9 1.0 H1 A:G1005 4.4 11.0 1.0 C5 A:U1006 4.6 9.8 1.0 SR A:SR9001 4.6 7.0 0.2 N1 A:G1005 4.7 8.2 1.0 O A:HOH9120 4.7 38.3 1.0 C2 A:U1006 4.8 10.2 1.0 H5 A:U1006 5.0 16.5 1.0

Sodium binding site 3 out of 4 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:Na2103 b:8.9 occ:0.05 NA B:NA2103 0.0 8.9 0.1 NA B:NA2103 2.4 13.5 0.2 O B:HOH2225 3.2 44.0 1.0 O4 B:U2006 3.2 14.6 0.9 H3 B:U2006 3.6 18.9 0.9 C4 B:U2006 3.7 14.1 0.9 N3 B:U2006 3.8 14.9 0.9 NA A:NA9003 4.0 9.9 0.1 C5 B:U2006 4.6 13.2 0.9 C2 B:U2006 4.7 16.6 0.9 H5 B:U2006 5.0 48.0 0.9

Sodium binding site 4 out of 4 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 B:Na2103 b:13.5 occ:0.20 NA B:NA2103 0.0 13.5 0.2 O4 B:U2006 2.3 14.6 0.9 NA B:NA2103 2.4 8.9 0.1 H3 B:U2006 3.1 18.9 0.9 C4 B:U2006 3.3 14.1 0.9 N3 B:U2006 3.6 14.9 0.9 O6 B:G2005 3.7 7.9 1.0 C6 B:G2005 4.2 7.7 1.0 H1 B:G2005 4.2 10.3 1.0 SR B:SR2102 4.4 6.8 0.2 N1 B:G2005 4.5 8.0 1.0 C5 B:U2006 4.6 13.2 0.9 C2 B:U2006 4.9 16.6 0.9 O B:HOH2225 4.9 44.0 1.0 H5 B:U2006 5.0 48.0 0.9

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