Sodium in PDB 2elg: The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius

The structure of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius, PDB code: 2elg was solved by H.Ohishi, Y.Tozuka, D.Y.Zhou, T.Ishida, K.Nakatani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	17.847, 30.988, 44.022, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 24.7

The structure of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius (pdb code 2elg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius, PDB code: 2elg:

Sodium binding site 1 out of 1 in the The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Rare Crystallographic Structure of D(Cgcgcg)2: the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)2 at 10 Degree Celsius within 5.0Å range: probe atom residue distance (Å) B Occ A:Na116 b:2.0 occ:1.00 O A:HOH15 2.3 5.6 1.0 O A:HOH55 2.4 17.0 1.0 H2 A:HOH15 2.6 15.0 1.0 H1 A:HOH55 2.9 15.0 1.0 H1 A:HOH15 3.2 15.0 1.0 H2 A:HOH55 3.3 15.0 1.0 H92 A:SPD120 3.8 15.0 1.0 H102 A:SPD120 4.0 15.0 1.0 H1 A:HOH36 4.1 15.0 1.0 O A:HOH85 4.2 12.0 1.0 H12 A:SPD120 4.2 15.0 1.0 OP1 A:DG6 4.3 3.8 1.0 OP2 A:DC5 4.3 3.8 1.0 O5' A:DG6 4.4 2.9 1.0 N10 A:SPD120 4.5 13.2 1.0 C9 A:SPD120 4.6 12.0 1.0 H1 A:HOH85 4.6 15.0 1.0 C5' A:DC5 4.6 2.0 1.0 H2 A:HOH36 4.9 15.0 1.0 O4' A:DG6 4.9 2.5 1.0 H2 A:HOH85 4.9 15.0 1.0 O5' A:DC5 5.0 2.4 1.0

H.Ohishi, Y.Tozuka, Z.Da-Yang, T.Ishida, K.Nakatani. The Rare Crystallographic Structure of D(Cgcgcg)(2): the Natural Spermidine Molecule Bound to the Minor Groove of Left-Handed Z-Dna D(Cgcgcg)(2) at 10 Degrees C Biochem.Biophys.Res.Commun. V. 358 24 2007.
ISSN: ISSN 0006-291X
PubMed: 17467661
DOI: 10.1016/J.BBRC.2007.04.026