Summary information

PDB id
8gp7
Class
DNA
Method
NMR
Summary
Structure of trioxacarcin a covalently bound to ret g4-DNA
Reference
Yin S, Cao C: "Structure of Trioxacarcin A covalently bound to RET G4-DNA."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=ssss sugar=3.3. groove=---- planarity=0.179 type=other  nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2 glyco-bond=---- sugar=333. groove=---- planarity=0.179 type=other  nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3 glyco-bond=---- sugar=3-33 groove=---- planarity=0.174 type=other  nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ssss sugar=3.3. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=333. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=12.29 rise=4.19 twist=19.7
  step#2  pm(>>,forward)  area=17.20 rise=4.03 twist=23.0
  strand#1 DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- sugar=.3- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=s-- sugar=..3 nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams
 1  glyco-bond=ssss sugar=3.3. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
2 glyco-bond=---- sugar=333. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
step#1 mm(<>,outward) area=12.29 rise=4.19 twist=19.7

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 2  glyco-bond=---- sugar=333. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
3 glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
step#2 pm(>>,forward) area=17.20 rise=4.03 twist=23.0

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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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=ssss sugar=3.3. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=333. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=12.29 rise=4.19 twist=19.7
  step#2  pm(>>,forward)  area=17.20 rise=4.03 twist=23.0
  strand#1  U DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- sugar=.3- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=s-- sugar=..3 nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=3 GCG A.DG4,A.DC5,A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 C A.DC10
  loop#3 type=propeller strands=[#3,#4] nts=3 GCG A.DG14,A.DC15,A.DG16

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