2F8W

Crystal structure of d(CACGTG)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interaction between the Z-Type DNA Duplex and 1,3-Propanediamine: Crystal Structure of d(CACGTG)2 at 1.2 A Resolution

Narayana, N.Shamala, N.Ganesh, K.N.Viswamitra, M.A.

(2006) Biochemistry 45: 1200-1211

  • DOI: 10.1021/bi051569l

  • PubMed Abstract: 
  • The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 A resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. The ...

    The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 A resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C(3)H(10)N(2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.


    Related Citations: 
    • Structure of d(CACGTG), Z-DNA hexamer containing AT base pairs
      Coll, M.,Fita, I.,Lloveras, J.,Subirana, J.A.,Bardella, F.,Huynh-Dinh, T.,Igolen, J.
      (1988) Nucleic Acids Res. 16: 8695
    • Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.
      Harper, A.,Brannigan, J.A.,Buck, M.,Hewitt, L.,Lewis, R.J.,Moore, M.H.,Schneider, B.
      (1998) Acta Crystallogr.,Sect.D 54: 1273
    • Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms
      Thiyagarajan, S.,Rajan, S.S.,Gautham, N.
      (2004) Nucleic Acids Res. 32: 5945
    • Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature
      Thiyagarajan, S.,Satheesh Kumar, P.,Rajan, S.S.,Gautham, N.
      (2002) Acta Crystallogr.,Sect.D 58: 1381
    • Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-resolution
      Egli, M.,Williams, L.D.,Gao, Q.,Rich, A.
      (1991) Biochemistry 30: 11388
    • Sequence-dependent microheterogeneity of Z-DNA: The crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG)
      Sadasivan, C.,Gautham, N.
      (1995) J.Mol.Biol. 248: 918


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA. nxn17@case.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*AP*CP*GP*TP*G)-3'A,B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
13D
Query on 13D

Download SDF File 
Download CCD File 
B
1,3-DIAMINOPROPANE
C3 H10 N2
XFNJVJPLKCPIBV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 18.420α = 90.00
b = 30.740β = 90.00
c = 43.180γ = 90.00
Software Package:
Software NamePurpose
CAD4data reduction
CAD4data scaling
X-PLORmodel building
X-PLORphasing
CAD4data collection
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance