Summary information

PDB id
7d33
Class
DNA
Method
X-ray (2.117 Å)
Summary
The pb2+ complexed structure of tba g8c mutant
Reference
Liu H, Gao Y, Mathivanan J, Shen F, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Sheng J, Gan J (2022): "Structure-guided development of Pb 2+ -binding DNA aptamers." Sci Rep, 12, 460. doi: 10.1038/s41598-021-04243-2.
Abstract
Owing to its great threat to human health and environment, Pb2+ pollution has been recognized as a major public problem by the World Health Organization (WHO). Many DNA aptamers have been utilized in the development of Pb2+-detection sensors, but the underlying mechanisms remain elusive. Here, we report three Pb2+-complexed structures of the thrombin binding aptamer (TBA). These high-resolution crystal structures showed that TBA forms intramolecular G-quadruplex and Pb2+ is bound by the two G-tetrads in the center. Compared to K+-stabilized G-quadruplexes, the coordinating distance between Pb2+ and the G-tetrads are much shorter. The T3T4 and T12T13 linkers play important roles in dimerization and crystallization of TBA, but they are changeable for Pb2+-binding. In combination with mutagenesis and CD spectra, the G8C mutant structure unraveled that the T7G8T9 linker of TBA is also variable. In addition to expansion of the Pb2+-binding aptamer sequences, our study also set up one great example for quick and rational development of other aptamers with similar or optimized binding activity.
G4 notes
10 G-tetrads, 5 G4 helices, 5 G4 stems, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 10 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.397 type=bowl-2 nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.442 type=bowl-2 nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.428 type=bowl-2 nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.431 type=bowl-2 nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
 5 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.403 type=bowl-2 nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6
 6 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.432 type=bowl-2 nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5
 7 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.406 type=bowl-2 nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6
 8 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.420 type=bowl-2 nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5
 9 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.412 type=bowl-2 nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
10 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.419 type=bowl-2 nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5

List of 5 G4-helices

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3

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Helix#3, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5
  step#1  mm(<>,outward)  area=17.05 rise=3.55 twist=13.5
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG C.DG1,C.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG C.DG15,C.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG C.DG10,C.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG C.DG6,C.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5
  step#1  mm(<>,outward)  area=17.05 rise=3.55 twist=13.5

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=18.36 rise=3.55 twist=12.6
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG1,D.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG15,D.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG6,D.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=18.36 rise=3.55 twist=12.6

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Helix#5, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
  step#1  mm(<>,outward)  area=17.82 rise=3.53 twist=13.4
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG E.DG1,E.DG2
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG E.DG15,E.DG14
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG E.DG10,E.DG11
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG E.DG6,E.DG5

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
  step#1  mm(<>,outward)  area=17.82 rise=3.53 twist=13.4

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List of 5 G4-stems

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, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5
  step#1  mm(<>,outward)  area=18.73 rise=3.54 twist=12.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT A.DT3,A.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT A.DT7,A.DC8,A.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT A.DT12,A.DT13

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
  step#1  mm(<>,outward)  area=18.53 rise=3.55 twist=13.3
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT B.DT3,B.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT B.DT7,B.DC8,B.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT B.DT12,B.DT13

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Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG C.DG1,C.DG15,C.DG10,C.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG C.DG2,C.DG14,C.DG11,C.DG5
  step#1  mm(<>,outward)  area=17.05 rise=3.55 twist=13.5
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG C.DG1,C.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG C.DG15,C.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG C.DG10,C.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG C.DG6,C.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT C.DT3,C.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT C.DT7,C.DC8,C.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT C.DT12,C.DT13

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Stem#4, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG D.DG1,D.DG15,D.DG10,D.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG D.DG2,D.DG14,D.DG11,D.DG5
  step#1  mm(<>,outward)  area=18.36 rise=3.55 twist=12.6
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG1,D.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG15,D.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG10,D.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG6,D.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT D.DT3,D.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT D.DT7,D.DC8,D.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT D.DT12,D.DT13

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Stem#5, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG E.DG1,E.DG15,E.DG10,E.DG6
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG E.DG2,E.DG14,E.DG11,E.DG5
  step#1  mm(<>,outward)  area=17.82 rise=3.53 twist=13.4
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG E.DG1,E.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG E.DG15,E.DG14
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG E.DG10,E.DG11
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG E.DG6,E.DG5
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT E.DT3,E.DT4
  loop#2 type=lateral   strands=[#4,#3] nts=3 TCT E.DT7,E.DC8,E.DT9
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT E.DT12,E.DT13

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