Summary information and primary citation

PDB-id
2hbn
Class
DNA
Method
X-ray (1.55 Å)
Summary
Crystallization of the tl+-form of the oxytricha nova g-quadruplex
Reference
Gill ML, Strobel SA, Loria JP (2006): "Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex." Nucleic Acids Res., 34, 4506-4514. doi: 10.1093/nar/gkl616.
Abstract
The crystal structure of the Tl+ form of the G-quadruplex formed from the Oxytricha nova telomere sequence, d(G4T4G4), has been solved to 1.55 A. This G-quadruplex contains five Tl+ ions, three of which are interspersed between adjacent G-quartet planes and one in each of the two thymine loops. The structure displays a high degree of similarity to the K+ crystal structure [Haider et al. (2002), J. Mol. Biol., 320, 189-200], including the number and location of the monovalent cation binding sites. The highly isomorphic nature of the two structures, which contain such a large number of monovalent binding sites (relative to nucleic acid content), verifies the ability of Tl+ to mimic K+ in nucleic acids. Information from this report confirms and extends the assignment of 205Tl resonances from a previous report [Gill et al. (2005), J. Am. Chem. Soc., 127, 16 723-16 732] where 205Tl NMR was used to study monovalent cation binding to this G-quadruplex. The assignment of these resonances provides evidence for the occurrence of conformational dynamics in the thymine loop region that is in slow exchange on the 205Tl timescale.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2

Cartoon-block schematics in six views (download the tarball)

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List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.205 type=other  -- nts=4 GGGG 1:A.DG1,1:B.DG4,1:A.DG12,1:B.DG9
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.157 type=planar -- nts=4 GGGG 1:A.DG2,1:B.DG3,1:A.DG11,1:B.DG10
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.153 type=planar -- nts=4 GGGG 1:A.DG3,1:B.DG2,1:A.DG10,1:B.DG11
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.233 type=other  -- nts=4 GGGG 1:A.DG4,1:B.DG1,1:A.DG9,1:B.DG12

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, 4 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG4,1:A.DG12,1:B.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG3,1:A.DG11,1:B.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG2,1:A.DG10,1:B.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG1,1:A.DG9,1:B.DG12
  step#1  mm(<>,outward)  area=15.12 rise=3.45 twist=17.9
  step#2  pp(><,inward)   area=17.96 rise=3.55 twist=36.7
  step#3  mm(<>,outward)  area=15.75 rise=3.52 twist=16.9
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG4,1:B.DG3,1:B.DG2,1:B.DG1
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9
  strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG9,1:B.DG10,1:B.DG11,1:B.DG12

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG4,1:A.DG12,1:B.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG3,1:A.DG11,1:B.DG10
  step#1  mm(<>,outward)  area=15.12 rise=3.45 twist=17.9

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 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG3,1:A.DG11,1:B.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG2,1:A.DG10,1:B.DG11
  step#2  pp(><,inward)   area=17.96 rise=3.55 twist=36.7

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 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG2,1:A.DG10,1:B.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG1,1:A.DG9,1:B.DG12
  step#3  mm(<>,outward)  area=15.75 rise=3.52 twist=16.9

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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, 4 G-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG4,1:A.DG12,1:B.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG3,1:A.DG11,1:B.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG2,1:A.DG10,1:B.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG1,1:A.DG9,1:B.DG12
  step#1  mm(<>,outward)  area=15.12 rise=3.45 twist=17.9
  step#2  pp(><,inward)   area=17.96 rise=3.55 twist=36.7
  step#3  mm(<>,outward)  area=15.75 rise=3.52 twist=16.9
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG4,1:B.DG3,1:B.DG2,1:B.DG1
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG9,1:B.DG10,1:B.DG11,1:B.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT 1:A.DT5,1:A.DT6,1:A.DT7,1:A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT 1:B.DT5,1:B.DT6,1:B.DT7,1:B.DT8

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