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

PDB-id
352d
Class
DNA
Method
X-ray (0.95 Å)
Summary
The crystal structure of a parallel-stranded parallel-stranded guanine tetraplex at 0.95 angstrom resolution
Reference
Phillips, K., Dauter, Z., Murchie, A.I., Lilley, D.M., Luisi, B.: (1997) "The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution." J.Mol.Biol., 273, 171-182.
Abstract
In both DNA and RNA, stretches of guanine bases can form stable four-stranded helices in the presence of sodium or potassium ions. Sequences with a propensity to form guanine tetraplexes have been found in chromosomal telomers, immunoglobulin switch regions, and recombination sites. We report the crystal structure at 0.95 A resolution of a parallel-stranded tetraplex formed by the hexanucleotide d(TG4T) in the presence of sodium ions. The four strands form a right-handed helix that is stabilized by hydrogen-bonding tetrads of co-planar guanine bases. Well-resolved sodium ions are found between and, at defined points, within tetrad planes and are coordinated with the guanine O6 groups. Nine calcium ions have been identified, each with a well-defined hepta-coordinate hydration shell. Hydrogen-bonding water patterns are observed within the tetraplex's helical grooves and clustered about the phosphate groups. Water molecules in the groove may form a hydrogen bond with the O4', and may affect the stacking behavior of guanine. Two distinct stacking arrangements are noted for the guanine tetrads. The thymine bases do not contribute to the four-stranded conformation, but instead stack to stabilize the crystal lattice. We present evidence that the sugar conformation is strained and propose that this originates from forces that optimize guanine base stacking. Discrete conformational disorder is observed at several places in the phosphodiester backbone, which results from a simple crankshaft rotation that requires no net change in the sugar conformation.
G4 notes
16 G-tetrads, 2 G4 helices, 4 G4 stems, 2 G4 coaxial stacks · parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

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List of 16 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.224 type=bowl   nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
 2 glyco-bond=---- groove=---- planarity=0.210 type=bowl   nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 3 glyco-bond=---- groove=---- planarity=0.257 type=bowl   nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4 glyco-bond=---- groove=---- planarity=0.306 type=bowl   nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
 5 glyco-bond=---- groove=---- planarity=0.050 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52
 6 glyco-bond=---- groove=---- planarity=0.229 type=bowl   nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 7 glyco-bond=---- groove=---- planarity=0.241 type=bowl   nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 8 glyco-bond=---- groove=---- planarity=0.261 type=bowl   nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55
 9 glyco-bond=---- groove=---- planarity=0.050 type=planar nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92
10 glyco-bond=---- groove=---- planarity=0.232 type=bowl   nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
11 glyco-bond=---- groove=---- planarity=0.240 type=bowl   nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
12 glyco-bond=---- groove=---- planarity=0.231 type=bowl   nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95
13 glyco-bond=---- groove=---- planarity=0.219 type=bowl   nts=4 GGGG M.DG122,P.DG152,O.DG142,N.DG132
14 glyco-bond=---- groove=---- planarity=0.210 type=bowl   nts=4 GGGG M.DG123,P.DG153,O.DG143,N.DG133
15 glyco-bond=---- groove=---- planarity=0.226 type=bowl   nts=4 GGGG M.DG124,P.DG154,O.DG144,N.DG134
16 glyco-bond=---- groove=---- planarity=0.306 type=bowl   nts=4 GGGG M.DG125,P.DG155,O.DG145,N.DG135

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG52,G.DG62,H.DG72,E.DG42
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG53,G.DG63,H.DG73,E.DG43
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG54,G.DG64,H.DG74,E.DG44
 8  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG55,G.DG65,H.DG75,E.DG45
  step#1  mp(<<,backward) area=11.62 rise=3.37 twist=27.8
  step#2  mp(<<,backward) area=12.34 rise=3.29 twist=26.7
  step#3  mp(<<,backward) area=8.82  rise=3.31 twist=31.7
  step#4  mm(<>,outward)  area=13.11 rise=3.47 twist=17.4
  step#5  pm(>>,forward)  area=7.01  rise=3.44 twist=34.8
  step#6  pm(>>,forward)  area=10.57 rise=3.31 twist=29.3
  step#7  pm(>>,forward)  area=11.05 rise=3.35 twist=28.4
  strand#1 DNA glyco-bond=-------- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,F.DG52,F.DG53,F.DG54,F.DG55
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG D.DG35,D.DG34,D.DG33,D.DG32,G.DG62,G.DG63,G.DG64,G.DG65
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG C.DG25,C.DG24,C.DG23,C.DG22,H.DG72,H.DG73,H.DG74,H.DG75
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG B.DG15,B.DG14,B.DG13,B.DG12,E.DG42,E.DG43,E.DG44,E.DG45

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
step#1 mp(<<,backward) area=11.62 rise=3.37 twist=27.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
step#2 mp(<<,backward) area=12.34 rise=3.29 twist=26.7

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
step#3 mp(<<,backward) area=8.82 rise=3.31 twist=31.7

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG52,G.DG62,H.DG72,E.DG42
step#4 mm(<>,outward) area=13.11 rise=3.47 twist=17.4

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG52,G.DG62,H.DG72,E.DG42
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG53,G.DG63,H.DG73,E.DG43
step#5 pm(>>,forward) area=7.01 rise=3.44 twist=34.8

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG53,G.DG63,H.DG73,E.DG43
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG54,G.DG64,H.DG74,E.DG44
step#6 pm(>>,forward) area=10.57 rise=3.31 twist=29.3

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG54,G.DG64,H.DG74,E.DG44
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG F.DG55,G.DG65,H.DG75,E.DG45
step#7 pm(>>,forward) area=11.05 rise=3.35 twist=28.4

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG122,N.DG132,O.DG142,P.DG152
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG123,N.DG133,O.DG143,P.DG153
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG124,N.DG134,O.DG144,P.DG154
 8  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG125,N.DG135,O.DG145,P.DG155
  step#1  mp(<<,backward) area=11.70 rise=3.32 twist=28.0
  step#2  mp(<<,backward) area=10.48 rise=3.31 twist=29.7
  step#3  mp(<<,backward) area=7.03  rise=3.45 twist=34.8
  step#4  mm(<>,outward)  area=13.98 rise=3.46 twist=16.8
  step#5  pm(>>,forward)  area=8.59  rise=3.32 twist=32.1
  step#6  pm(>>,forward)  area=11.29 rise=3.29 twist=27.9
  step#7  pm(>>,forward)  area=12.52 rise=3.38 twist=26.8
  strand#1 DNA glyco-bond=-------- nts=8 GGGGGGGG I.DG85,I.DG84,I.DG83,I.DG82,M.DG122,M.DG123,M.DG124,M.DG125
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG L.DG115,L.DG114,L.DG113,L.DG112,N.DG132,N.DG133,N.DG134,N.DG135
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG K.DG105,K.DG104,K.DG103,K.DG102,O.DG142,O.DG143,O.DG144,O.DG145
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG J.DG95,J.DG94,J.DG93,J.DG92,P.DG152,P.DG153,P.DG154,P.DG155

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
step#1 mp(<<,backward) area=11.70 rise=3.32 twist=28.0

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
step#2 mp(<<,backward) area=10.48 rise=3.31 twist=29.7

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92
step#3 mp(<<,backward) area=7.03 rise=3.45 twist=34.8

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG122,N.DG132,O.DG142,P.DG152
step#4 mm(<>,outward) area=13.98 rise=3.46 twist=16.8

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG122,N.DG132,O.DG142,P.DG152
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG123,N.DG133,O.DG143,P.DG153
step#5 pm(>>,forward) area=8.59 rise=3.32 twist=32.1

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG123,N.DG133,O.DG143,P.DG153
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG124,N.DG134,O.DG144,P.DG154
step#6 pm(>>,forward) area=11.29 rise=3.29 twist=27.9

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG124,N.DG134,O.DG144,P.DG154
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG M.DG125,N.DG135,O.DG145,P.DG155
step#7 pm(>>,forward) area=12.52 rise=3.38 twist=26.8

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List of 4 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.DG2,D.DG32,C.DG22,B.DG12
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
  step#1  pm(>>,forward)  area=8.82  rise=3.31 twist=31.7
  step#2  pm(>>,forward)  area=12.34 rise=3.29 twist=26.7
  step#3  pm(>>,forward)  area=11.62 rise=3.37 twist=27.8
  strand#1  U DNA glyco-bond=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG32,D.DG33,D.DG34,D.DG35
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG22,C.DG23,C.DG24,C.DG25
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG12,B.DG13,B.DG14,B.DG15

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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.DG42,H.DG72,G.DG62,F.DG52
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55
  step#1  pm(>>,forward)  area=7.01  rise=3.44 twist=34.8
  step#2  pm(>>,forward)  area=10.57 rise=3.31 twist=29.3
  step#3  pm(>>,forward)  area=11.05 rise=3.35 twist=28.4
  strand#1  U DNA glyco-bond=---- nts=4 GGGG E.DG42,E.DG43,E.DG44,E.DG45
  strand#2  U DNA glyco-bond=---- nts=4 GGGG H.DG72,H.DG73,H.DG74,H.DG75
  strand#3  U DNA glyco-bond=---- nts=4 GGGG G.DG62,G.DG63,G.DG64,G.DG65
  strand#4  U DNA glyco-bond=---- nts=4 GGGG F.DG52,F.DG53,F.DG54,F.DG55

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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.DG82,L.DG112,K.DG102,J.DG92
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95
  step#1  pm(>>,forward)  area=7.03  rise=3.45 twist=34.8
  step#2  pm(>>,forward)  area=10.48 rise=3.31 twist=29.7
  step#3  pm(>>,forward)  area=11.70 rise=3.32 twist=28.0
  strand#1  U DNA glyco-bond=---- nts=4 GGGG I.DG82,I.DG83,I.DG84,I.DG85
  strand#2  U DNA glyco-bond=---- nts=4 GGGG L.DG112,L.DG113,L.DG114,L.DG115
  strand#3  U DNA glyco-bond=---- nts=4 GGGG K.DG102,K.DG103,K.DG104,K.DG105
  strand#4  U DNA glyco-bond=---- nts=4 GGGG J.DG92,J.DG93,J.DG94,J.DG95

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG122,P.DG152,O.DG142,N.DG132
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG123,P.DG153,O.DG143,N.DG133
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG124,P.DG154,O.DG144,N.DG134
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG125,P.DG155,O.DG145,N.DG135
  step#1  pm(>>,forward)  area=8.59  rise=3.32 twist=32.1
  step#2  pm(>>,forward)  area=11.29 rise=3.29 twist=27.9
  step#3  pm(>>,forward)  area=12.52 rise=3.38 twist=26.8
  strand#1  U DNA glyco-bond=---- nts=4 GGGG M.DG122,M.DG123,M.DG124,M.DG125
  strand#2  U DNA glyco-bond=---- nts=4 GGGG P.DG152,P.DG153,P.DG154,P.DG155
  strand#3  U DNA glyco-bond=---- nts=4 GGGG O.DG142,O.DG143,O.DG144,O.DG145
  strand#4  U DNA glyco-bond=---- nts=4 GGGG N.DG132,N.DG133,N.DG134,N.DG135

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List of 2 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']
 2 G4 helix#2 contains 2 G4 stems: [#3,#4]  [5'/5']

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