Sodium in PDB 293d: Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex, PDB code: 293d was solved by H.Ohishi, I.Nakanishi, K.Inubushi, G.A.Van Der Marel, J.H.Vanboom, A.Rich, A.H.-J.Wang, T.Hakoshima, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	17.930, 31.230, 44.640, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex (pdb code 293d). 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 Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex, PDB code: 293d:

Sodium binding site 1 out of 1 in the Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Interaction Between the Left-Handed Z-Dna and Polyamine-2: the Crystal Structure of the D(Cg)3 and Spermidine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na17 b:25.0 occ:1.00 O A:HOH108 2.1 37.4 1.0 O A:HOH112 2.2 43.8 1.0 O A:HOH109 2.2 30.6 1.0 O A:HOH110 2.3 42.6 1.0 O A:HOH107 2.4 38.4 1.0 O A:HOH111 2.5 36.0 1.0 O A:HOH58 3.4 33.8 1.0 OP1 A:DG6 4.0 10.3 1.0 O5' A:DG6 4.6 7.4 1.0 OP2 A:DC5 4.6 9.6 1.0 C5' A:DC5 4.8 3.9 1.0 P A:DG6 4.9 7.7 1.0

H.Ohishi, I.Nakanishi, K.Inubushi, G.Van Der Marel, J.H.Van Boom, A.Rich, A.H.Wang, T.Hakoshima, K.Tomita. Interaction Between the Left-Handed Z-Dna and Polyamine-2. the Crystal Structure of the D(Cg)3 and Spermidine Complex. Febs Lett. V. 391 153 1996.
ISSN: ISSN 0014-5793
PubMed: 8706905
DOI: 10.1016/0014-5793(96)00723-5