Summary information

PDB id
1bub
Class
DNA
Method
NMR
Summary
Determination of internuclear angles of DNA using paramagnetic assisted magnetic alignment
Reference
Beger RD, Marathias VM, Volkman BF, Bolton PH (1998): "Determination of internuclear angles of DNA using paramagnetic-assisted magnetic alignment." J.Magn.Reson., 135, 256-259. doi: 10.1006/jmre.1998.1527.
Abstract
Paramagnetic ions have been used to assist the magnetic alignment of DNA. The anisotropy of the binding sites is sufficient to give rise to significant alignment of the DNA with the observed proton-carbon dipolar couplings spanning a 70-Hz range. The dipolar couplings have been used to determine the positions of the axial and rhombic alignment axes. The positions of the alignment axes relative to the positions of the binding sites of the paramagnetic europium ions have also been determined.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=3.-. groove=wnwn planarity=0.443 type=bowl   nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2 glyco-bond=-s-s sugar=.-.- groove=wnwn planarity=0.179 type=other  nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=3.-. groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=.-.- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.33 rise=3.32 twist=18.5
  strand#1 DNA glyco-bond=s- sugar=3. nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=.- nts=2 GG A.DG15,A.DG14
  strand#3 DNA glyco-bond=s- sugar=-. nts=2 GG A.DG10,A.DG11
  strand#4 DNA glyco-bond=-s sugar=.- nts=2 GG A.DG6,A.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=3.-. groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=.-.- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.33 rise=3.32 twist=18.5

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=3.-. groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=.-.- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=14.33 rise=3.32 twist=18.5
  strand#1  U DNA glyco-bond=s- sugar=3. nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=.- nts=2 GG A.DG15,A.DG14
  strand#3  U DNA glyco-bond=s- sugar=-. nts=2 GG A.DG10,A.DG11
  strand#4  D DNA glyco-bond=-s sugar=.- nts=2 GG A.DG6,A.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT A.DT3,A.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT A.DT7,A.DG8,A.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT A.DT12,A.DT13

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