Summary information

PDB id
8t8t
Class
DNA
Method
X-ray (1.62 Å)
Summary
Crystal structure of tet25 in complex with pydh2 ligand in p212121 space group
Reference
Lam G, Yatunsyk LA: "Crystal structure of TET25 in complex with PyDH2 ligand in P212121 space group."
Abstract
 
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems, 4(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

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List of 8 G-tetrads

 1 glyco-bond=s-s- sugar=-.-- groove=wnwn planarity=0.457 type=other  nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.447 type=other  nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12
 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.423 type=other  nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11
 4 glyco-bond=-s-s sugar=-.-- groove=wnwn planarity=0.480 type=bowl-2 nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10
 5 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.417 type=other  nts=4 GGGG B.DG4,B.DG25,B.DG16,B.DG13
 6 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.430 type=other  nts=4 GGGG B.DG5,B.DG24,B.DG17,B.DG12
 7 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.392 type=bowl-2 nts=4 GGGG B.DG6,B.DG23,B.DG18,B.DG11
 8 glyco-bond=-s-s sugar=.--- groove=wnwn planarity=0.475 type=bowl-2 nts=4 GGGG B.DG7,B.DG22,B.DG19,B.DG10

List of 2 G4-helices

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=-.-- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11
 4  glyco-bond=-s-s sugar=-.-- groove=wnwn WC-->Major nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10
  step#1  mm(<>,outward)  area=15.96 rise=3.51 twist=15.5
  step#2  pp(><,inward)   area=0.00  rise=6.61 twist=22.6
  step#3  mm(<>,outward)  area=19.17 rise=3.44 twist=12.9
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7
  strand#2 DNA glyco-bond=-s-s sugar=.--. nts=4 GGGG A.DG25,A.DG24,A.DG23,A.DG22
  strand#3 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19
  strand#4 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG13,A.DG12,A.DG11,A.DG10

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3 stacking diagrams 
 1  glyco-bond=s-s- sugar=-.-- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12
  step#1  mm(<>,outward)  area=15.96 rise=3.51 twist=15.5

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 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11
  step#2  pp(><,inward)   area=0.00  rise=6.61 twist=22.6

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 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11
 4  glyco-bond=-s-s sugar=-.-- groove=wnwn WC-->Major nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10
  step#3  mm(<>,outward)  area=19.17 rise=3.44 twist=12.9

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Helix#2, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG4,B.DG25,B.DG16,B.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG5,B.DG24,B.DG17,B.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG6,B.DG23,B.DG18,B.DG11
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG B.DG7,B.DG22,B.DG19,B.DG10
  step#1  mm(<>,outward)  area=17.23 rise=3.48 twist=15.5
  step#2  pp(><,inward)   area=0.00  rise=6.59 twist=23.2
  step#3  mm(<>,outward)  area=19.11 rise=3.59 twist=10.9
  strand#1 DNA glyco-bond=s-s- sugar=---. nts=4 GGGG B.DG4,B.DG5,B.DG6,B.DG7
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG25,B.DG24,B.DG23,B.DG22
  strand#3 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG16,B.DG17,B.DG18,B.DG19
  strand#4 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG13,B.DG12,B.DG11,B.DG10

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3 stacking diagrams 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG4,B.DG25,B.DG16,B.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG5,B.DG24,B.DG17,B.DG12
  step#1  mm(<>,outward)  area=17.23 rise=3.48 twist=15.5

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 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG5,B.DG24,B.DG17,B.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG6,B.DG23,B.DG18,B.DG11
  step#2  pp(><,inward)   area=0.00  rise=6.59 twist=23.2

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 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG6,B.DG23,B.DG18,B.DG11
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG B.DG7,B.DG22,B.DG19,B.DG10
  step#3  mm(<>,outward)  area=19.11 rise=3.59 twist=10.9

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List of 2 G4-stems

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-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 4(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=-.-- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11
 4  glyco-bond=-s-s sugar=-.-- groove=wnwn WC-->Major nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10
  step#1  mm(<>,outward)  area=15.96 rise=3.51 twist=15.5
  step#2  pp(><,inward)   area=0.00  rise=6.61 twist=22.6
  step#3  mm(<>,outward)  area=19.17 rise=3.44 twist=12.9
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7
  strand#2  D DNA glyco-bond=-s-s sugar=.--. nts=4 GGGG A.DG25,A.DG24,A.DG23,A.DG22
  strand#3  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19
  strand#4  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG13,A.DG12,A.DG11,A.DG10
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT A.DT8,A.DT9
  loop#2 type=lateral   strands=[#4,#3] nts=2 TT A.DT14,A.DT15
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT A.DT20,A.DT21

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Stem#2, 4 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 4(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG4,B.DG25,B.DG16,B.DG13
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG5,B.DG24,B.DG17,B.DG12
 3  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG6,B.DG23,B.DG18,B.DG11
 4  glyco-bond=-s-s sugar=.--- groove=wnwn WC-->Major nts=4 GGGG B.DG7,B.DG22,B.DG19,B.DG10
  step#1  mm(<>,outward)  area=17.23 rise=3.48 twist=15.5
  step#2  pp(><,inward)   area=0.00  rise=6.59 twist=23.2
  step#3  mm(<>,outward)  area=19.11 rise=3.59 twist=10.9
  strand#1  U DNA glyco-bond=s-s- sugar=---. nts=4 GGGG B.DG4,B.DG5,B.DG6,B.DG7
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG25,B.DG24,B.DG23,B.DG22
  strand#3  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG16,B.DG17,B.DG18,B.DG19
  strand#4  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG13,B.DG12,B.DG11,B.DG10
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT B.DT8,B.DT9
  loop#2 type=lateral   strands=[#4,#3] nts=2 TT B.DT14,B.DT15
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT B.DT20,B.DT21

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