Summary information and primary citation

PDB-id
9u3i
Class
DNA
Method
X-ray (1.2 Å)
Summary
Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer
Reference
Park S, Kanazawa H, Kondo J: "Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)

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

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.611 type=other  O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.597 type=other  O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=14.89 rise=3.52 twist=14.3
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG1,1:B.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG15,1:B.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG10,1:B.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG6,1:B.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=14.89 rise=3.52 twist=14.3

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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-tetrads, 3 loops, INTRA-molecular, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG 1:B.DG1,1:B.DG15,1:B.DG10,1:B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG 1:B.DG2,1:B.DG14,1:B.DG11,1:B.DG5
  step#1  mm(<>,outward)  area=14.89 rise=3.52 twist=14.3
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG1,1:B.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG15,1:B.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG 1:B.DG10,1:B.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG 1:B.DG6,1:B.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 ?T 1:B.A1L8S3,1:B.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT 1:B.DT7,1:B.DG8,1:B.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT 1:B.DT12,1:B.DT13

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