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

PDB-id
2gwq
Class
DNA
Method
X-ray (2.0 Å)
Summary
Crystal structure of d(g4t4g4) with four quadruplexes in the asymmetric unit
Reference
Lee, M.P.H., Haider, S., Parkinson, G.N., Neidle, S.: "Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit." To be published
Abstract
 
G4 notes
16 G-tetrads, 4 G4 helices, 4 G4 stems · (2+2), UDDU

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=s--s groove=w-n- planarity=0.255 type=bowl   nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2 glyco-bond=-ss- groove=w-n- planarity=0.116 type=planar nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3 glyco-bond=s--s groove=w-n- planarity=0.112 type=planar nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4 glyco-bond=-ss- groove=w-n- planarity=0.240 type=other  nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
 5 glyco-bond=s--s groove=w-n- planarity=0.244 type=other  nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
 6 glyco-bond=-ss- groove=w-n- planarity=0.098 type=planar nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 7 glyco-bond=s--s groove=w-n- planarity=0.094 type=planar nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 8 glyco-bond=-ss- groove=w-n- planarity=0.271 type=bowl   nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
 9 glyco-bond=s--s groove=w-n- planarity=0.234 type=other  nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69
10 glyco-bond=-ss- groove=w-n- planarity=0.118 type=planar nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70
11 glyco-bond=s--s groove=w-n- planarity=0.119 type=planar nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71
12 glyco-bond=-ss- groove=w-n- planarity=0.235 type=bowl   nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72
13 glyco-bond=s--s groove=w-n- planarity=0.288 type=bowl   nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93
14 glyco-bond=-ss- groove=w-n- planarity=0.102 type=planar nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94
15 glyco-bond=s--s groove=w-n- planarity=0.127 type=planar nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95
16 glyco-bond=-ss- groove=w-n- planarity=0.245 type=other  nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96

List of 4 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=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.33 rise=3.49 twist=17.3
  step#2  pp(><,inward)   area=20.17 rise=3.56 twist=36.5
  step#3  mm(<>,outward)  area=13.64 rise=3.46 twist=17.9
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
step#1 mm(<>,outward) area=14.33 rise=3.49 twist=17.3

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
step#2 pp(><,inward) area=20.17 rise=3.56 twist=36.5

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
step#3 mm(<>,outward) area=13.64 rise=3.46 twist=17.9

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
  step#1  mm(<>,outward)  area=12.90 rise=3.52 twist=18.0
  step#2  pp(><,inward)   area=19.52 rise=3.52 twist=36.7
  step#3  mm(<>,outward)  area=13.25 rise=3.44 twist=17.7
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
step#1 mm(<>,outward) area=12.90 rise=3.52 twist=18.0

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
step#2 pp(><,inward) area=19.52 rise=3.52 twist=36.7

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
step#3 mm(<>,outward) area=13.25 rise=3.44 twist=17.7

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Helix#3, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72
  step#1  mm(<>,outward)  area=13.14 rise=3.49 twist=17.5
  step#2  pp(><,inward)   area=20.49 rise=3.55 twist=37.0
  step#3  mm(<>,outward)  area=13.57 rise=3.45 twist=17.8
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG E.DG49,E.DG50,E.DG51,E.DG52
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG F.DG64,F.DG63,F.DG62,F.DG61
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG E.DG60,E.DG59,E.DG58,E.DG57
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG F.DG69,F.DG70,F.DG71,F.DG72

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70
step#1 mm(<>,outward) area=13.14 rise=3.49 twist=17.5

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71
step#2 pp(><,inward) area=20.49 rise=3.55 twist=37.0

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72
step#3 mm(<>,outward) area=13.57 rise=3.45 twist=17.8

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Helix#4, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96
  step#1  mm(<>,outward)  area=14.40 rise=3.50 twist=16.9
  step#2  pp(><,inward)   area=19.23 rise=3.55 twist=36.8
  step#3  mm(<>,outward)  area=13.48 rise=3.46 twist=18.0
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG G.DG73,G.DG74,G.DG75,G.DG76
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG H.DG88,H.DG87,H.DG86,H.DG85
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG G.DG84,G.DG83,G.DG82,G.DG81
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG H.DG93,H.DG94,H.DG95,H.DG96

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94
step#1 mm(<>,outward) area=14.40 rise=3.50 twist=16.9

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95
step#2 pp(><,inward) area=19.23 rise=3.55 twist=36.8

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96
step#3 mm(<>,outward) area=13.48 rise=3.46 twist=18.0

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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, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.33 rise=3.49 twist=17.3
  step#2  pp(><,inward)   area=20.17 rise=3.56 twist=36.5
  step#3  mm(<>,outward)  area=13.64 rise=3.46 twist=17.9
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20

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

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
  step#1  mm(<>,outward)  area=12.90 rise=3.52 twist=18.0
  step#2  pp(><,inward)   area=19.52 rise=3.52 twist=36.7
  step#3  mm(<>,outward)  area=13.25 rise=3.44 twist=17.7
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT C.DT29,C.DT30,C.DT31,C.DT32
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT D.DT41,D.DT42,D.DT43,D.DT44

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Stem#3, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72
  step#1  mm(<>,outward)  area=13.14 rise=3.49 twist=17.5
  step#2  pp(><,inward)   area=20.49 rise=3.55 twist=37.0
  step#3  mm(<>,outward)  area=13.57 rise=3.45 twist=17.8
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG E.DG49,E.DG50,E.DG51,E.DG52
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG F.DG64,F.DG63,F.DG62,F.DG61
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG E.DG60,E.DG59,E.DG58,E.DG57
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG F.DG69,F.DG70,F.DG71,F.DG72
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT E.DT53,E.DT54,E.DT55,E.DT56
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT F.DT65,F.DT66,F.DT67,F.DT68

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

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96
  step#1  mm(<>,outward)  area=14.40 rise=3.50 twist=16.9
  step#2  pp(><,inward)   area=19.23 rise=3.55 twist=36.8
  step#3  mm(<>,outward)  area=13.48 rise=3.46 twist=18.0
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG G.DG73,G.DG74,G.DG75,G.DG76
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG H.DG88,H.DG87,H.DG86,H.DG85
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG G.DG84,G.DG83,G.DG82,G.DG81
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG H.DG93,H.DG94,H.DG95,H.DG96
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT G.DT77,G.DT78,G.DT79,G.DT80
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT H.DT89,H.DT90,H.DT91,H.DT92

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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