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

PDB-id
4wo3
Class
DNA
Method
X-ray (2.73 Å)
Summary
The second c-kit DNA quadruplex crystal structure
Reference
Wei, D., Neidle, S.: "THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE." To be published
Abstract
 
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 2(-PX+P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'-SEPARATED

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

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.175 type=other  nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
 2 glyco-bond=---- groove=---- planarity=0.206 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 3 glyco-bond=---- groove=---- planarity=0.332 type=bowl   nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
 4 glyco-bond=---- groove=---- planarity=0.156 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
 5 glyco-bond=---- groove=---- planarity=0.204 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 6 glyco-bond=---- groove=---- planarity=0.309 type=bowl   nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15

List of 1 G4-helix [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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG15,A.DG22,A.DG8,A.DG4
  step#1  mp(<<,backward) area=9.98  rise=3.36 twist=32.3
  step#2  mp(<<,backward) area=14.54 rise=3.46 twist=28.8
  step#3  mm(<>,outward)  area=29.35 rise=3.32 twist=-10.5
  step#4  pm(>>,forward)  area=12.90 rise=3.39 twist=29.6
  step#5  pm(>>,forward)  area=9.86  rise=3.40 twist=32.9
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG B.DG4,B.DG3,B.DG2,A.DG13,A.DG14,A.DG15
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG B.DG8,B.DG7,B.DG6,A.DG10,A.DG21,A.DG22
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG B.DG22,B.DG21,B.DG10,A.DG6,A.DG7,A.DG8
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG B.DG15,B.DG14,B.DG13,A.DG2,A.DG3,A.DG4

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
step#1 mp(<<,backward) area=9.98 rise=3.36 twist=32.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
step#2 mp(<<,backward) area=14.54 rise=3.46 twist=28.8

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2
step#3 mm(<>,outward) area=29.35 rise=3.32 twist=-10.5

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3
step#4 pm(>>,forward) area=12.90 rise=3.39 twist=29.6

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG15,A.DG22,A.DG8,A.DG4
step#5 pm(>>,forward) area=9.86 rise=3.40 twist=32.9

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List of 2 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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
  step#1  pm(>>,forward)  area=9.98  rise=3.36 twist=32.3
  strand#1  U DNA glyco-bond=-- nts=2 GG B.DG3,B.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG B.DG7,B.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG21,B.DG22
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG B.DA5,B.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG B.DC9,B.DG10,B.DC11,B.DT12,B.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG B.DA16,B.DG17,B.DG18,B.DA19,B.DG20

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=9.86  rise=3.40 twist=32.9
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG A.DC9,A.DG10,A.DC11,A.DT12,A.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20

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

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

List of 4 non-stem G4-loops (including the two closing Gs)

 1* type=V-shaped  helix=#1 nts=5 GGGCG B.DG6,B.DG7,B.DG8,B.DC9,B.DG10
 2 type=lateral   helix=#1 nts=4 GCTG B.DG10,B.DC11,B.DT12,B.DG13
 3* type=V-shaped  helix=#1 nts=5 GGGCG A.DG6,A.DG7,A.DG8,A.DC9,A.DG10
 4 type=lateral   helix=#1 nts=4 GCTG A.DG10,A.DC11,A.DT12,A.DG13