Sodium in PDB 4r44: Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex

The structure of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex, PDB code: 4r44 was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.89 / 2.69
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	38.940, 39.000, 84.080, 103.34, 103.37, 90.04
R / Rfree (%)	29.4 / 32.5

The structure of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex also contains other interesting chemical elements:

Potassium

(K)

14 atoms

The binding sites of Sodium atom in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex (pdb code 4r44). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex, PDB code: 4r44:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ K:Na101 b:26.4 occ:1.00 C5' K:DT21 3.7 37.3 1.0 C4' K:DT21 4.3 37.2 1.0 C4' P:DG72 4.4 29.3 1.0 C5' K:DG22 4.6 30.8 1.0 O3' P:DG72 4.6 26.9 1.0 O5' P:DG72 4.7 33.9 1.0 OP1 K:DG22 4.7 37.3 1.0 C5' P:DG72 4.8 30.9 1.0 O5' K:DT21 4.9 32.3 1.0

Sodium binding site 2 out of 4 in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ N:Na102 b:24.9 occ:1.00 OP1 N:DG53 1.9 31.7 1.0 P N:DG53 3.3 33.6 1.0 O5' N:DG53 3.8 37.2 1.0 OP2 N:DG53 4.1 31.9 1.0 O3' N:DG52 4.5 31.0 1.0 C5' N:DG53 4.5 29.6 1.0 C5' O:DG65 4.5 40.9 1.0 C4' O:DG65 4.8 43.7 1.0

Sodium binding site 3 out of 4 in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ O:Na101 b:24.7 occ:1.00 OP1 O:DG63 2.1 22.8 1.0 P O:DG63 3.6 23.2 1.0 O3' O:DG62 4.3 23.5 1.0 O5' O:DG63 4.5 29.8 1.0 OP2 O:DG63 4.6 22.1 1.0 C5' O:DG63 4.7 25.9 1.0

Sodium binding site 4 out of 4 in the Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Racemic Crystal Structure of A Tetramolecular Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ P:Na102 b:64.2 occ:1.00 OP1 P:DG73 2.4 26.4 1.0 P P:DG73 3.9 29.2 1.0 O3' P:DG72 4.4 26.9 1.0 O5' P:DG73 4.7 29.2 1.0 OP2 P:DG73 4.9 26.0 1.0

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014