Summary information

PDB id
4u92
Class
DNA
Method
X-ray (1.5 Å)
Summary
Crystal structure of a DNA-ba2+ g-quadruplex containing a water-mediated c-tetrad
Reference
Zhang D, Huang T, Lukeman PS, Paukstelis PJ (2014): "Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad." Nucleic Acids Res., 42, 13422-13429. doi: 10.1093/nar/gku1122.
Abstract
We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.
G4 notes
8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 3'/3'

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 8 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.105 type=planar nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl   nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.256 type=other  nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.065 type=planar nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.085 type=planar nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.217 type=bowl   nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.244 type=other  nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.046 type=planar nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10

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, 8 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9
 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10
 5  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10
 6  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9
 7  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 8  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
  step#1  pm(>>,forward)  area=0.00  rise=7.07 twist=53.4
  step#2  pm(>>,forward)  area=13.65 rise=3.23 twist=28.7
  step#3  pm(>>,forward)  area=12.83 rise=3.39 twist=28.9
  step#4  pp(><,inward)   area=30.87 rise=3.46 twist=-160.5
  step#5  mp(<<,backward) area=11.57 rise=3.44 twist=30.2
  step#6  mp(<<,backward) area=14.52 rise=3.24 twist=28.3
  step#7  mp(<<,backward) area=0.00  rise=7.03 twist=53.1
  strand#1 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 1:A.DG5,1:A.DG7,1:A.DG9,1:A.DG10,1:B.DG10,1:B.DG9,1:B.DG7,1:B.DG5
  strand#2 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 4:A.DG5,4:A.DG7,4:A.DG9,4:A.DG10,3:B.DG10,3:B.DG9,3:B.DG7,3:B.DG5
  strand#3 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 2:A.DG5,2:A.DG7,2:A.DG9,2:A.DG10,2:B.DG10,2:B.DG9,2:B.DG7,2:B.DG5
  strand#4 DNA glyco-bond=-------- sugar=--3--3-- nts=8 GGGGGGGG 3:A.DG5,3:A.DG7,3:A.DG9,3:A.DG10,4:B.DG10,4:B.DG9,4:B.DG7,4:B.DG5

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7 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,4:A.DG5,2:A.DG5,3:A.DG5
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7
  step#1  pm(>>,forward)  area=0.00  rise=7.07 twist=53.4

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG7,4:A.DG7,2:A.DG7,3:A.DG7
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9
  step#2  pm(>>,forward)  area=13.65 rise=3.23 twist=28.7

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 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9
 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10
  step#3  pm(>>,forward)  area=12.83 rise=3.39 twist=28.9

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 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10
 5  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10
  step#4  pp(><,inward)   area=30.87 rise=3.46 twist=-160.5

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 5  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10
 6  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9
  step#5  mp(<<,backward) area=11.57 rise=3.44 twist=30.2

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 6  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9
 7  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
  step#6  mp(<<,backward) area=14.52 rise=3.24 twist=28.3

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 7  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7
 8  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5
  step#7  mp(<<,backward) area=0.00  rise=7.03 twist=53.1

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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, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.DG9,4:A.DG9,2:A.DG9,3:A.DG9
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG10,4:A.DG10,2:A.DG10,3:A.DG10
  step#1  pm(>>,forward)  area=12.83 rise=3.39 twist=28.9
  strand#1  U DNA glyco-bond=-- sugar=3- nts=2 GG 1:A.DG9,1:A.DG10
  strand#2  U DNA glyco-bond=-- sugar=3- nts=2 GG 4:A.DG9,4:A.DG10
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG 2:A.DG9,2:A.DG10
  strand#4  U DNA glyco-bond=-- sugar=3- nts=2 GG 3:A.DG9,3:A.DG10

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Stem#2, 2 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.DG9,3:B.DG9,2:B.DG9,4:B.DG9
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG10,3:B.DG10,2:B.DG10,4:B.DG10
  step#1  pm(>>,forward)  area=11.57 rise=3.44 twist=30.2
  strand#1  U DNA glyco-bond=-- sugar=3- nts=2 GG 1:B.DG9,1:B.DG10
  strand#2  U DNA glyco-bond=-- sugar=3- nts=2 GG 3:B.DG9,3:B.DG10
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG 2:B.DG9,2:B.DG10
  strand#4  U DNA glyco-bond=-- sugar=3- nts=2 GG 4:B.DG9,4:B.DG10

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List of 1 G4 coaxial stack

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [3'/3']