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

PDB-id
244d
Class
DNA
Method
X-ray (1.2 Å)
Summary
The high-resolution crystal structure of a parallel-stranded guanine tetraplex
Reference
Laughlan, G., Murchie, A.I., Norman, D.G., Moore, M.H., Moody, P.C., Lilley, D.M., Luisi, B.: (1994) "The high-resolution crystal structure of a parallel-stranded guanine tetraplex." Science, 265, 520-524.
Abstract
Repeat tracts of guanine bases found in DNA and RNA can form tetraplex structures in the presence of a variety of monovalent cations. Evidence suggests that guanine tetraplexes assume important functions within chromosomal telomeres, immunoglobulin switch regions, and the human immunodeficiency virus genome. The structure of a parallel-stranded tetraplex formed by the hexanucleotide d(TG4T) and stabilized by sodium cations was determined by x-ray crystallography to 1.2 angstroms resolution. Sharply resolved sodium cations were found between and within planes of hydrogen-bonded guanine quartets, and an ordered groove hydration was observed. Distinct intra- and intermolecular stacking arrangements were adopted by the guanine quartets. Thymine bases were exclusively involved in making extensive lattice contacts.
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]

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---- groove=---- planarity=0.214 type=bowl   nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
 2 glyco-bond=---- groove=---- planarity=0.200 type=bowl   nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 3 glyco-bond=---- groove=---- planarity=0.237 type=bowl   nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4 glyco-bond=---- groove=---- planarity=0.289 type=bowl   nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
 5 glyco-bond=---- groove=---- planarity=0.041 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52
 6 glyco-bond=---- groove=---- planarity=0.216 type=bowl   nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 7 glyco-bond=---- groove=---- planarity=0.246 type=bowl   nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 8 glyco-bond=---- groove=---- planarity=0.255 type=bowl   nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55
 9 glyco-bond=---- groove=---- planarity=0.045 type=planar nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92
10 glyco-bond=---- groove=---- planarity=0.228 type=bowl   nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93
11 glyco-bond=---- groove=---- planarity=0.238 type=bowl   nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94
12 glyco-bond=---- groove=---- planarity=0.236 type=bowl   nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95
13 glyco-bond=---- groove=---- planarity=0.218 type=bowl   nts=4 GGGG M.DG122,P.DG152,O.DG142,N.DG132
14 glyco-bond=---- groove=---- planarity=0.199 type=bowl   nts=4 GGGG M.DG123,P.DG153,O.DG143,N.DG133
15 glyco-bond=---- groove=---- planarity=0.220 type=bowl   nts=4 GGGG M.DG124,P.DG154,O.DG144,N.DG134
16 glyco-bond=---- groove=---- planarity=0.283 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=11.28 rise=3.45 twist=27.8
  step#2  mp(<<,backward) area=11.73 rise=3.36 twist=27.2
  step#3  mp(<<,backward) area=8.98  rise=3.36 twist=31.8
  step#4  mm(<>,outward)  area=13.29 rise=3.55 twist=17.4
  step#5  pm(>>,forward)  area=7.10  rise=3.51 twist=34.4
  step#6  pm(>>,forward)  area=10.63 rise=3.39 twist=29.1
  step#7  pm(>>,forward)  area=10.61 rise=3.40 twist=28.6
  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=11.28 rise=3.45 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=11.73 rise=3.36 twist=27.2

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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=8.98 rise=3.36 twist=31.8

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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=13.29 rise=3.55 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=7.10 rise=3.51 twist=34.4

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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=10.63 rise=3.39 twist=29.1

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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=10.61 rise=3.40 twist=28.6

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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=10.98 rise=3.40 twist=28.3
  step#2  mp(<<,backward) area=10.85 rise=3.38 twist=29.3
  step#3  mp(<<,backward) area=7.16  rise=3.52 twist=34.7
  step#4  mm(<>,outward)  area=13.66 rise=3.55 twist=17.1
  step#5  pm(>>,forward)  area=8.70  rise=3.37 twist=32.0
  step#6  pm(>>,forward)  area=11.83 rise=3.35 twist=27.3
  step#7  pm(>>,forward)  area=11.58 rise=3.45 twist=27.7
  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=10.98 rise=3.40 twist=28.3

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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=10.85 rise=3.38 twist=29.3

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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=7.16 rise=3.52 twist=34.7

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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=13.66 rise=3.55 twist=17.1

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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=8.70 rise=3.37 twist=32.0

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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=11.83 rise=3.35 twist=27.3

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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=11.58 rise=3.45 twist=27.7

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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=8.98  rise=3.36 twist=31.8
  step#2  pm(>>,forward)  area=11.73 rise=3.36 twist=27.2
  step#3  pm(>>,forward)  area=11.28 rise=3.45 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=7.10  rise=3.51 twist=34.4
  step#2  pm(>>,forward)  area=10.63 rise=3.39 twist=29.1
  step#3  pm(>>,forward)  area=10.61 rise=3.40 twist=28.6
  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=7.16  rise=3.52 twist=34.7
  step#2  pm(>>,forward)  area=10.85 rise=3.38 twist=29.3
  step#3  pm(>>,forward)  area=10.98 rise=3.40 twist=28.3
  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=8.70  rise=3.37 twist=32.0
  step#2  pm(>>,forward)  area=11.83 rise=3.35 twist=27.3
  step#3  pm(>>,forward)  area=11.58 rise=3.45 twist=27.7
  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)