Summary information

PDB id
6up0
Class
RNA
Method
X-ray (2.8 Å)
Summary
Structure of the mango-iii fluorescent aptamer bound to yo3-biotin
Reference
Trachman RJ, Ferre-D'Amare AR: "RNA aptamer FRET pair."
Abstract
 
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, 2(-P-P-Lw), (3+1), UUUD

Base-block schematics in six views

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List of 4 G-tetrads

 1 glyco-bond=---s groove=--wn planarity=0.492 type=other  nts=4 GGGG C.G9,C.G13,C.G18,C.G25
 2 glyco-bond=---s groove=--wn planarity=0.274 type=other  nts=4 GGGG C.G10,C.G14,C.G19,C.G23
 3 glyco-bond=---s groove=--wn planarity=0.521 type=other  nts=4 GGGG D.G9,D.G13,D.G18,D.G25
 4 glyco-bond=---s groove=--wn planarity=0.280 type=other  nts=4 GGGG D.G10,D.G14,D.G19,D.G23

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

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G10,C.G14,C.G19,C.G23
  step#1  pm(>>,forward)  area=11.01 rise=3.42 twist=29.6
  strand#1 RNA glyco-bond=-- nts=2 GG C.G9,C.G10
  strand#2 RNA glyco-bond=-- nts=2 GG C.G13,C.G14
  strand#3 RNA glyco-bond=-- nts=2 GG C.G18,C.G19
  strand#4 RNA glyco-bond=ss nts=2 GG C.G25,C.G23

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G10,C.G14,C.G19,C.G23
step#1 pm(>>,forward) area=11.01 rise=3.42 twist=29.6

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

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G10,D.G14,D.G19,D.G23
  step#1  pm(>>,forward)  area=10.20 rise=3.44 twist=29.2
  strand#1 RNA glyco-bond=-- nts=2 GG D.G9,D.G10
  strand#2 RNA glyco-bond=-- nts=2 GG D.G13,D.G14
  strand#3 RNA glyco-bond=-- nts=2 GG D.G18,D.G19
  strand#4 RNA glyco-bond=ss nts=2 GG D.G25,D.G23

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1 stacking diagram
 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G10,D.G14,D.G19,D.G23
step#1 pm(>>,forward) area=10.20 rise=3.44 twist=29.2

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, hybrid-(mixed), 2(-P-P-Lw), (3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G9,C.G13,C.G18,C.G25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG C.G10,C.G14,C.G19,C.G23
  step#1  pm(>>,forward)  area=11.01 rise=3.42 twist=29.6
  strand#1  U RNA glyco-bond=-- nts=2 GG C.G9,C.G10
  strand#2  U RNA glyco-bond=-- nts=2 GG C.G13,C.G14
  strand#3  U RNA glyco-bond=-- nts=2 GG C.G18,C.G19
  strand#4* D RNA glyco-bond=ss nts=2 GG C.G25,C.G23 bulged-nts=1 U C.U24
  loop#1 type=propeller strands=[#1,#2] nts=2 AA C.A11,C.A12
  loop#2 type=propeller strands=[#2,#3] nts=3 AUU C.A15,C.U16,C.U17
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU C.U20,C.A21,C.U22

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUD, hybrid-(mixed), 2(-P-P-Lw), (3+1)

 1  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G9,D.G13,D.G18,D.G25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG D.G10,D.G14,D.G19,D.G23
  step#1  pm(>>,forward)  area=10.20 rise=3.44 twist=29.2
  strand#1  U RNA glyco-bond=-- nts=2 GG D.G9,D.G10
  strand#2  U RNA glyco-bond=-- nts=2 GG D.G13,D.G14
  strand#3  U RNA glyco-bond=-- nts=2 GG D.G18,D.G19
  strand#4* D RNA glyco-bond=ss nts=2 GG D.G25,D.G23 bulged-nts=1 U D.U24
  loop#1 type=propeller strands=[#1,#2] nts=2 AA D.A11,D.A12
  loop#2 type=propeller strands=[#2,#3] nts=3 AUU D.A15,D.U16,D.U17
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU D.U20,D.A21,D.U22

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