Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
1s47
Class
DNA
Method
X-ray (2.5 Å)
Summary
Crystal structure analysis of the DNA quadruplex d(tggggt)s2
Reference
Caceres, C., Wright, G., Gouyette, C., Parkinson, G., Subirana, J.A.: (2004) "A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions." Nucleic Acids Res., 32, 1097-1102.
Abstract
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG1-3) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3'ends of the quadruplexes; (iv) a thymine tetrad between two guanine tetrads. Thymines are stabilized in pairs by single hydrogen bonds. A central sodium ion interacts with two thymines and contributes to the tetrad structure. (v) Completely disordered thymines which do not show any clear location in the crystal. The tetrads are stabilized by either Na+ or Tl+ ions. We show that by using MAD methods, Tl+ can be unambiguously located and distinguished from Na+. We can thus determine the preference for either ion in each ionic site of the structure under the conditions used by us.
G4 notes
12 G-tetrads, 2 G4 helices, 3 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 5'/5'

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 12 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.152 type=planar nts=4 GGGG A.DG102,D.DG432,C.DG322,B.DG212
 2 glyco-bond=---- groove=---- planarity=0.186 type=bowl-2 nts=4 GGGG A.DG103,D.DG433,C.DG323,B.DG213
 3 glyco-bond=---- groove=---- planarity=0.173 type=other  nts=4 GGGG A.DG104,D.DG434,C.DG324,B.DG214
 4 glyco-bond=---- groove=---- planarity=0.280 type=bowl   nts=4 GGGG A.DG105,D.DG435,C.DG325,B.DG215
 5 glyco-bond=---- groove=---- planarity=0.096 type=planar nts=4 GGGG E.DG582,H.DG912,G.DG802,F.DG692
 6 glyco-bond=---- groove=---- planarity=0.236 type=other  nts=4 GGGG E.DG583,H.DG913,G.DG803,F.DG693
 7 glyco-bond=---- groove=---- planarity=0.165 type=other  nts=4 GGGG E.DG584,H.DG914,G.DG804,F.DG694
 8 glyco-bond=---- groove=---- planarity=0.245 type=bowl   nts=4 GGGG E.DG585,H.DG915,G.DG805,F.DG695
 9 glyco-bond=---- groove=---- planarity=0.331 type=bowl   nts=4 GGGG I.DG1022,L.DG1352,K.DG1242,J.DG1132
10 glyco-bond=---- groove=---- planarity=0.246 type=bowl   nts=4 GGGG I.DG1023,L.DG1353,K.DG1243,J.DG1133
11 glyco-bond=---- groove=---- planarity=0.242 type=other  nts=4 GGGG I.DG1024,L.DG1354,K.DG1244,J.DG1134
12 glyco-bond=---- groove=---- planarity=0.237 type=other  nts=4 GGGG I.DG1025,L.DG1355,K.DG1245,J.DG1135

List of 2 G4-helices [summary · schematics · tetrads · stems · costacks · homepage]

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, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,D.DG432,C.DG322,B.DG212
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,D.DG433,C.DG323,B.DG213
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG104,D.DG434,C.DG324,B.DG214
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG105,D.DG435,C.DG325,B.DG215
  step#1  pm(>>,forward)  area=16.35 rise=3.25 twist=24.5
  step#2  pm(>>,forward)  area=9.58  rise=3.30 twist=33.1
  step#3  pm(>>,forward)  area=10.61 rise=3.37 twist=27.0
  strand#1 DNA glyco-bond=---- nts=4 GGGG A.DG102,A.DG103,A.DG104,A.DG105
  strand#2 DNA glyco-bond=---- nts=4 GGGG D.DG432,D.DG433,D.DG434,D.DG435
  strand#3 DNA glyco-bond=---- nts=4 GGGG C.DG322,C.DG323,C.DG324,C.DG325
  strand#4 DNA glyco-bond=---- nts=4 GGGG B.DG212,B.DG213,B.DG214,B.DG215

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3 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,D.DG432,C.DG322,B.DG212
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,D.DG433,C.DG323,B.DG213
step#1 pm(>>,forward) area=16.35 rise=3.25 twist=24.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,D.DG433,C.DG323,B.DG213
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG104,D.DG434,C.DG324,B.DG214
step#2 pm(>>,forward) area=9.58 rise=3.30 twist=33.1

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG104,D.DG434,C.DG324,B.DG214
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG105,D.DG435,C.DG325,B.DG215
step#3 pm(>>,forward) area=10.61 rise=3.37 twist=27.0

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG585,H.DG915,G.DG805,F.DG695
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG584,H.DG914,G.DG804,F.DG694
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG583,H.DG913,G.DG803,F.DG693
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG582,H.DG912,G.DG802,F.DG692
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1022,J.DG1132,K.DG1242,L.DG1352
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1023,J.DG1133,K.DG1243,L.DG1353
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1024,J.DG1134,K.DG1244,L.DG1354
 8  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1025,J.DG1135,K.DG1245,L.DG1355
  step#1  mp(<<,backward) area=13.84 rise=3.44 twist=26.3
  step#2  mp(<<,backward) area=9.84  rise=3.47 twist=31.2
  step#3  mp(<<,backward) area=10.46 rise=3.62 twist=28.4
  step#4  mm(<>,outward)  area=11.57 rise=3.75 twist=19.3
  step#5  pm(>>,forward)  area=11.33 rise=3.37 twist=29.8
  step#6  pm(>>,forward)  area=11.74 rise=3.34 twist=28.9
  step#7  pm(>>,forward)  area=12.22 rise=3.41 twist=28.0
  strand#1 DNA glyco-bond=-------- nts=8 GGGGGGGG E.DG585,E.DG584,E.DG583,E.DG582,I.DG1022,I.DG1023,I.DG1024,I.DG1025
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG H.DG915,H.DG914,H.DG913,H.DG912,J.DG1132,J.DG1133,J.DG1134,J.DG1135
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG G.DG805,G.DG804,G.DG803,G.DG802,K.DG1242,K.DG1243,K.DG1244,K.DG1245
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG F.DG695,F.DG694,F.DG693,F.DG692,L.DG1352,L.DG1353,L.DG1354,L.DG1355

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG585,H.DG915,G.DG805,F.DG695
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG584,H.DG914,G.DG804,F.DG694
step#1 mp(<<,backward) area=13.84 rise=3.44 twist=26.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG584,H.DG914,G.DG804,F.DG694
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG583,H.DG913,G.DG803,F.DG693
step#2 mp(<<,backward) area=9.84 rise=3.47 twist=31.2

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG583,H.DG913,G.DG803,F.DG693
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG582,H.DG912,G.DG802,F.DG692
step#3 mp(<<,backward) area=10.46 rise=3.62 twist=28.4

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG582,H.DG912,G.DG802,F.DG692
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1022,J.DG1132,K.DG1242,L.DG1352
step#4 mm(<>,outward) area=11.57 rise=3.75 twist=19.3

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1022,J.DG1132,K.DG1242,L.DG1352
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1023,J.DG1133,K.DG1243,L.DG1353
step#5 pm(>>,forward) area=11.33 rise=3.37 twist=29.8

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1023,J.DG1133,K.DG1243,L.DG1353
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1024,J.DG1134,K.DG1244,L.DG1354
step#6 pm(>>,forward) area=11.74 rise=3.34 twist=28.9

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1024,J.DG1134,K.DG1244,L.DG1354
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG I.DG1025,J.DG1135,K.DG1245,L.DG1355
step#7 pm(>>,forward) area=12.22 rise=3.41 twist=28.0

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List of 3 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG102,D.DG432,C.DG322,B.DG212
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG103,D.DG433,C.DG323,B.DG213
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG104,D.DG434,C.DG324,B.DG214
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG105,D.DG435,C.DG325,B.DG215
  step#1  pm(>>,forward)  area=16.35 rise=3.25 twist=24.5
  step#2  pm(>>,forward)  area=9.58  rise=3.30 twist=33.1
  step#3  pm(>>,forward)  area=10.61 rise=3.37 twist=27.0
  strand#1  U DNA glyco-bond=---- nts=4 GGGG A.DG102,A.DG103,A.DG104,A.DG105
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG432,D.DG433,D.DG434,D.DG435
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG322,C.DG323,C.DG324,C.DG325
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG212,B.DG213,B.DG214,B.DG215

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG582,H.DG912,G.DG802,F.DG692
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG583,H.DG913,G.DG803,F.DG693
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG584,H.DG914,G.DG804,F.DG694
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG585,H.DG915,G.DG805,F.DG695
  step#1  pm(>>,forward)  area=10.46 rise=3.62 twist=28.4
  step#2  pm(>>,forward)  area=9.84  rise=3.47 twist=31.2
  step#3  pm(>>,forward)  area=13.84 rise=3.44 twist=26.3
  strand#1  U DNA glyco-bond=---- nts=4 GGGG E.DG582,E.DG583,E.DG584,E.DG585
  strand#2  U DNA glyco-bond=---- nts=4 GGGG H.DG912,H.DG913,H.DG914,H.DG915
  strand#3  U DNA glyco-bond=---- nts=4 GGGG G.DG802,G.DG803,G.DG804,G.DG805
  strand#4  U DNA glyco-bond=---- nts=4 GGGG F.DG692,F.DG693,F.DG694,F.DG695

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Stem#3, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG1022,L.DG1352,K.DG1242,J.DG1132
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG1023,L.DG1353,K.DG1243,J.DG1133
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG1024,L.DG1354,K.DG1244,J.DG1134
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG1025,L.DG1355,K.DG1245,J.DG1135
  step#1  pm(>>,forward)  area=11.33 rise=3.37 twist=29.8
  step#2  pm(>>,forward)  area=11.74 rise=3.34 twist=28.9
  step#3  pm(>>,forward)  area=12.22 rise=3.41 twist=28.0
  strand#1  U DNA glyco-bond=---- nts=4 GGGG I.DG1022,I.DG1023,I.DG1024,I.DG1025
  strand#2  U DNA glyco-bond=---- nts=4 GGGG L.DG1352,L.DG1353,L.DG1354,L.DG1355
  strand#3  U DNA glyco-bond=---- nts=4 GGGG K.DG1242,K.DG1243,K.DG1244,K.DG1245
  strand#4  U DNA glyco-bond=---- nts=4 GGGG J.DG1132,J.DG1133,J.DG1134,J.DG1135

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#2 contains 2 G4 stems: [#2,#3]  [5'/5']

List of 0 non-stem G4-loops (including the two closing Gs)