Summary information

PDB id
8u5j
Class
RNA
Method
X-ray (1.7 Å)
Summary
Structure of mango iii variant aptamer bound to t01-07m-b
Reference
Passalacqua LFM, Ferre-D'Amare AR: "Structure of Mango III variant aptamer bound to T01-07M-B."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-Lw), hybrid-2R(3+1), UUUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.510 type=other  nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.303 type=other  nts=4 GGGG A.G9,A.G13,A.G18,A.G22

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
  step#1  pm(>>,forward)  area=10.13 rise=3.46 twist=30.3
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG A.G8,A.G9
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG A.G12,A.G13
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG A.G17,A.G18
  strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG A.G24,A.G22

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1 stacking diagram 
 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
  step#1  pm(>>,forward)  area=10.13 rise=3.46 twist=30.3

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

 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major nts=4 GGGG A.G8,A.G12,A.G17,A.G24
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major nts=4 GGGG A.G9,A.G13,A.G18,A.G22
  step#1  pm(>>,forward)  area=10.13 rise=3.46 twist=30.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G8,A.G9
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG A.G12,A.G13
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG A.G17,A.G18
  strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG A.G24,A.G22 bulged-nts=1 U A.U23
  loop#1 type=propeller strands=[#1,#2] nts=2 AA A.A10,A.A11
  loop#2 type=propeller strands=[#2,#3] nts=3 UUU A.U14,A.U15,A.U16
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU A.U19,A.A20,A.U21

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