PDBsum entry 1s23

Go to PDB code: 
dna_rna metals links
Waters ×47
PDB id:
Name: DNA
Title: Crystal structure analysis of the b-DNA decamer cgcaattgcg
Structure: 5'-d( Cp Gp Cp Ap Ap Tp Tp Gp Cp G)-3'. Chain: a. Engineered: yes
Source: Synthetic: yes
1.60Å     R-factor:   0.216     R-free:   0.282
Authors: N.Valls,G.Wright,R.A.Steiner,G.N.Murshudov,J.A.Subirana
Key ref:
N.Valls et al. (2004). DNA variability in five crystal structures of d(CGCAATTGCG). Acta Crystallogr D Biol Crystallogr, 60, 680-685. PubMed id: 15039556 DOI: 10.1107/S0907444904002896
08-Jan-04     Release date:   06-Apr-04    


DOI no: 10.1107/S0907444904002896 Acta Crystallogr D Biol Crystallogr 60:680-685 (2004)
PubMed id: 15039556  
DNA variability in five crystal structures of d(CGCAATTGCG).
N.Valls, G.Wright, R.A.Steiner, G.N.Murshudov, J.A.Subirana.
The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.
  Selected figure(s)  
Figure 2.
Figure 2 Two neighbouring columns in the crystal structure. A cobalt ion (green) interacts with the N7 atom of two guanines. The bonds of the flipped-out residues in the central region are shown with a larger diameter. Hydration waters associated with the Co2+ ion are represented as red spheres.
Figure 3.
Figure 3 A detailed view of the interaction between the ends of two neighbouring duplexes (red and green) in a column. The flipped-out residues (C1 and G10) are shown in purple. Hydrogen bonds between G10 and G2 and between C1 and G8 are indicated as dashed lines.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 680-685) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481775 T.D.Fenn, M.J.Schnieders, M.Mustyakimov, C.Wu, P.Langan, V.S.Pande, and A.T.Brunger (2011).
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
  Structure, 19, 523-533.
PDB code: 3qba
19920127 B.Heddi, C.Oguey, C.Lavelle, N.Foloppe, and B.Hartmann (2010).
Intrinsic flexibility of B-DNA: the experimental TRX scale.
  Nucleic Acids Res, 38, 1034-1047.  
18253536 P.S.Pallan, D.Ittig, A.Héroux, Z.Wawrzak, C.J.Leumann, and M.Egli (2008).
Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles.
  Chem Commun (Camb), (), 883-885.
PDB code: 2rf3
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.