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

PDB-id
4r44
Class
DNA
Method
X-ray (2.69 Å)
Summary
Racemic crystal structure of a tetramolecular DNA G-quadruplex
Reference
Mandal, P.K., Collie, G.W., Kauffmann, B., Huc, I.: (2014) "Racemic DNA crystallography." Angew.Chem.Int.Ed.Engl., 53, 14424-14427.
Abstract
Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.
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=0.248 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=0.139 type=planar nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4 glyco-bond=---- groove=---- planarity=0.198 type=bowl   nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
 5 glyco-bond=---- groove=---- planarity=0.081 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52
 6 glyco-bond=---- groove=---- planarity=0.293 type=bowl   nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 7 glyco-bond=---- groove=---- planarity=0.201 type=bowl   nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 8 glyco-bond=---- groove=---- planarity=0.243 type=bowl   nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55
 9 glyco-bond=---- groove=---- planarity=0.208 type=bowl   nts=4 GGGG I.DG2,L.DG32,K.DG22,J.DG12
10 glyco-bond=---- groove=---- planarity=0.187 type=other  nts=4 GGGG I.DG3,L.DG33,K.DG23,J.DG13
11 glyco-bond=---- groove=---- planarity=0.155 type=planar nts=4 GGGG I.DG4,L.DG34,K.DG24,J.DG14
12 glyco-bond=---- groove=---- planarity=0.204 type=bowl   nts=4 GGGG I.DG5,L.DG35,K.DG25,J.DG15
13 glyco-bond=---- groove=---- planarity=0.071 type=planar nts=4 GGGG M.DG42,P.DG72,O.DG62,N.DG52
14 glyco-bond=---- groove=---- planarity=0.218 type=bowl   nts=4 GGGG M.DG43,P.DG73,O.DG63,N.DG53
15 glyco-bond=---- groove=---- planarity=0.204 type=bowl   nts=4 GGGG M.DG44,P.DG74,O.DG64,N.DG54
16 glyco-bond=---- groove=---- planarity=0.363 type=bowl   nts=4 GGGG M.DG45,P.DG75,O.DG65,N.DG55

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=12.14 rise=3.40 twist=28.2
  step#2  mp(<<,backward) area=10.01 rise=3.34 twist=31.6
  step#3  mp(<<,backward) area=10.79 rise=3.46 twist=28.4
  step#4  mm(<>,outward)  area=14.69 rise=3.70 twist=16.9
  step#5  pm(>>,forward)  area=8.95  rise=3.61 twist=29.5
  step#6  pm(>>,forward)  area=7.96  rise=3.42 twist=33.2
  step#7  pm(>>,forward)  area=11.99 rise=3.48 twist=26.2
  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=12.14 rise=3.40 twist=28.2

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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=10.01 rise=3.34 twist=31.6

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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=10.79 rise=3.46 twist=28.4

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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=14.69 rise=3.70 twist=16.9

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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=8.95 rise=3.61 twist=29.5

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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=7.96 rise=3.42 twist=33.2

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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=11.99 rise=3.48 twist=26.2

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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.DG5,L.DG35,K.DG25,J.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG4,L.DG34,K.DG24,J.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG3,L.DG33,K.DG23,J.DG13
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG2,L.DG32,K.DG22,J.DG12
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG52,O.DG62,P.DG72,M.DG42
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG53,O.DG63,P.DG73,M.DG43
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG54,O.DG64,P.DG74,M.DG44
 8  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG55,O.DG65,P.DG75,M.DG45
  step#1  mp(<<,backward) area=10.48 rise=3.38 twist=30.5
  step#2  mp(<<,backward) area=12.01 rise=3.39 twist=29.8
  step#3  mp(<<,backward) area=9.90  rise=3.42 twist=29.2
  step#4  mm(<>,outward)  area=13.85 rise=3.54 twist=17.0
  step#5  pm(>>,forward)  area=10.54 rise=3.75 twist=29.9
  step#6  pm(>>,forward)  area=8.44  rise=3.44 twist=32.0
  step#7  pm(>>,forward)  area=14.45 rise=3.43 twist=24.3
  strand#1 DNA glyco-bond=-------- nts=8 GGGGGGGG I.DG5,I.DG4,I.DG3,I.DG2,N.DG52,N.DG53,N.DG54,N.DG55
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG L.DG35,L.DG34,L.DG33,L.DG32,O.DG62,O.DG63,O.DG64,O.DG65
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG K.DG25,K.DG24,K.DG23,K.DG22,P.DG72,P.DG73,P.DG74,P.DG75
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG J.DG15,J.DG14,J.DG13,J.DG12,M.DG42,M.DG43,M.DG44,M.DG45

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG5,L.DG35,K.DG25,J.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG4,L.DG34,K.DG24,J.DG14
step#1 mp(<<,backward) area=10.48 rise=3.38 twist=30.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG4,L.DG34,K.DG24,J.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG3,L.DG33,K.DG23,J.DG13
step#2 mp(<<,backward) area=12.01 rise=3.39 twist=29.8

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG3,L.DG33,K.DG23,J.DG13
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG2,L.DG32,K.DG22,J.DG12
step#3 mp(<<,backward) area=9.90 rise=3.42 twist=29.2

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG2,L.DG32,K.DG22,J.DG12
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG52,O.DG62,P.DG72,M.DG42
step#4 mm(<>,outward) area=13.85 rise=3.54 twist=17.0

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG52,O.DG62,P.DG72,M.DG42
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG53,O.DG63,P.DG73,M.DG43
step#5 pm(>>,forward) area=10.54 rise=3.75 twist=29.9

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG53,O.DG63,P.DG73,M.DG43
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG54,O.DG64,P.DG74,M.DG44
step#6 pm(>>,forward) area=8.44 rise=3.44 twist=32.0

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG54,O.DG64,P.DG74,M.DG44
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG N.DG55,O.DG65,P.DG75,M.DG45
step#7 pm(>>,forward) area=14.45 rise=3.43 twist=24.3

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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=10.79 rise=3.46 twist=28.4
  step#2  pm(>>,forward)  area=10.01 rise=3.34 twist=31.6
  step#3  pm(>>,forward)  area=12.14 rise=3.40 twist=28.2
  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=8.95  rise=3.61 twist=29.5
  step#2  pm(>>,forward)  area=7.96  rise=3.42 twist=33.2
  step#3  pm(>>,forward)  area=11.99 rise=3.48 twist=26.2
  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.DG2,L.DG32,K.DG22,J.DG12
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG3,L.DG33,K.DG23,J.DG13
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG4,L.DG34,K.DG24,J.DG14
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG I.DG5,L.DG35,K.DG25,J.DG15
  step#1  pm(>>,forward)  area=9.90  rise=3.42 twist=29.2
  step#2  pm(>>,forward)  area=12.01 rise=3.39 twist=29.8
  step#3  pm(>>,forward)  area=10.48 rise=3.38 twist=30.5
  strand#1  U DNA glyco-bond=---- nts=4 GGGG I.DG2,I.DG3,I.DG4,I.DG5
  strand#2  U DNA glyco-bond=---- nts=4 GGGG L.DG32,L.DG33,L.DG34,L.DG35
  strand#3  U DNA glyco-bond=---- nts=4 GGGG K.DG22,K.DG23,K.DG24,K.DG25
  strand#4  U DNA glyco-bond=---- nts=4 GGGG J.DG12,J.DG13,J.DG14,J.DG15

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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.DG42,P.DG72,O.DG62,N.DG52
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG43,P.DG73,O.DG63,N.DG53
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG44,P.DG74,O.DG64,N.DG54
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG M.DG45,P.DG75,O.DG65,N.DG55
  step#1  pm(>>,forward)  area=10.54 rise=3.75 twist=29.9
  step#2  pm(>>,forward)  area=8.44  rise=3.44 twist=32.0
  step#3  pm(>>,forward)  area=14.45 rise=3.43 twist=24.3
  strand#1  U DNA glyco-bond=---- nts=4 GGGG M.DG42,M.DG43,M.DG44,M.DG45
  strand#2  U DNA glyco-bond=---- nts=4 GGGG P.DG72,P.DG73,P.DG74,P.DG75
  strand#3  U DNA glyco-bond=---- nts=4 GGGG O.DG62,O.DG63,O.DG64,O.DG65
  strand#4  U DNA glyco-bond=---- nts=4 GGGG N.DG52,N.DG53,N.DG54,N.DG55

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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)