Summary information

PDB id
6xt7
Class
DNA
Method
X-ray (1.56 Å)
Summary
Tel25 hybrid four-quartet g-quadruplex with k+
Reference
Li K, Yatsunyk L, Neidle S (2021): "Water spines and networks in G-quadruplex structures." Nucleic Acids Res., 49, 519-528. doi: 10.1093/nar/gkaa1177.
Abstract
Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.
G4 notes
16 G-tetrads, 4 G4 helices, 4 G4 stems, 3(-P-Lw-Ln), hybrid-1(3+1), UUDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 16 G-tetrads

 1 glyco-bond=s-ss sugar=3--- groove=wn-- planarity=0.202 type=other  nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004
 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.172 type=other  nts=4 GGGG A.DG1005,A.DG1010,A.DG1018,A.DG1023
 3 glyco-bond=--s- sugar=---. groove=-wn- planarity=0.182 type=other  nts=4 GGGG A.DG1006,A.DG1011,A.DG1017,A.DG1024
 4 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.353 type=bowl   nts=4 GGGG A.DG1007,A.DG1012,A.DG1016,A.DG1025
 5 glyco-bond=s-ss sugar=3--- groove=wn-- planarity=0.222 type=other  nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004
 6 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.183 type=other  nts=4 GGGG B.DG1005,B.DG1010,B.DG1018,B.DG1023
 7 glyco-bond=--s- sugar=---3 groove=-wn- planarity=0.180 type=other  nts=4 GGGG B.DG1006,B.DG1011,B.DG1017,B.DG1024
 8 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.332 type=bowl   nts=4 GGGG B.DG1007,B.DG1012,B.DG1016,B.DG1025
 9 glyco-bond=s-ss sugar=3.-- groove=wn-- planarity=0.206 type=other  nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004
10 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.188 type=other  nts=4 GGGG C.DG1005,C.DG1010,C.DG1018,C.DG1023
11 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.177 type=other  nts=4 GGGG C.DG1006,C.DG1011,C.DG1017,C.DG1024
12 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.382 type=bowl   nts=4 GGGG C.DG1007,C.DG1012,C.DG1016,C.DG1025
13 glyco-bond=s-ss sugar=3.-- groove=wn-- planarity=0.207 type=other  nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004
14 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.164 type=other  nts=4 GGGG D.DG1005,D.DG1010,D.DG1018,D.DG1023
15 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.161 type=other  nts=4 GGGG D.DG1006,D.DG1011,D.DG1017,D.DG1024
16 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.342 type=bowl   nts=4 GGGG D.DG1007,D.DG1012,D.DG1016,D.DG1025

List of 4 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, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG1010,A.DG1018,A.DG1023,A.DG1005
 3  glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major nts=4 GGGG A.DG1011,A.DG1017,A.DG1024,A.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG1012,A.DG1016,A.DG1025,A.DG1007
  step#1  mm(<>,outward)  area=15.61 rise=3.47 twist=15.5
  step#2  pm(>>,forward)  area=9.63  rise=3.43 twist=31.8
  step#3  pm(>>,forward)  area=14.07 rise=3.47 twist=24.5
  strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG A.DG1001,A.DG1010,A.DG1011,A.DG1012
  strand#2 DNA glyco-bond=-sss sugar=---- nts=4 GGGG A.DG1019,A.DG1018,A.DG1017,A.DG1016
  strand#3 DNA glyco-bond=s--- sugar=--.- nts=4 GGGG A.DG1022,A.DG1023,A.DG1024,A.DG1025
  strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG1004,A.DG1005,A.DG1006,A.DG1007

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3 stacking diagrams 
 1  glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC nts=4 GGGG A.DG1001,A.DG1019,A.DG1022,A.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG1010,A.DG1018,A.DG1023,A.DG1005
  step#1  mm(<>,outward)  area=15.61 rise=3.47 twist=15.5

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG1010,A.DG1018,A.DG1023,A.DG1005
 3  glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major nts=4 GGGG A.DG1011,A.DG1017,A.DG1024,A.DG1006
  step#2  pm(>>,forward)  area=9.63  rise=3.43 twist=31.8

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 3  glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major nts=4 GGGG A.DG1011,A.DG1017,A.DG1024,A.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG A.DG1012,A.DG1016,A.DG1025,A.DG1007
  step#3  pm(>>,forward)  area=14.07 rise=3.47 twist=24.5

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

 1  glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.DG1010,B.DG1018,B.DG1023,B.DG1005
 3  glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major nts=4 GGGG B.DG1011,B.DG1017,B.DG1024,B.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.DG1012,B.DG1016,B.DG1025,B.DG1007
  step#1  mm(<>,outward)  area=15.24 rise=3.51 twist=15.5
  step#2  pm(>>,forward)  area=8.90  rise=3.39 twist=31.9
  step#3  pm(>>,forward)  area=13.65 rise=3.49 twist=24.9
  strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG B.DG1001,B.DG1010,B.DG1011,B.DG1012
  strand#2 DNA glyco-bond=-sss sugar=---- nts=4 GGGG B.DG1019,B.DG1018,B.DG1017,B.DG1016
  strand#3 DNA glyco-bond=s--- sugar=--3- nts=4 GGGG B.DG1022,B.DG1023,B.DG1024,B.DG1025
  strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG B.DG1004,B.DG1005,B.DG1006,B.DG1007

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3 stacking diagrams 
 1  glyco-bond=s-ss sugar=3--- groove=wn-- Major-->WC nts=4 GGGG B.DG1001,B.DG1019,B.DG1022,B.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.DG1010,B.DG1018,B.DG1023,B.DG1005
  step#1  mm(<>,outward)  area=15.24 rise=3.51 twist=15.5

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.DG1010,B.DG1018,B.DG1023,B.DG1005
 3  glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major nts=4 GGGG B.DG1011,B.DG1017,B.DG1024,B.DG1006
  step#2  pm(>>,forward)  area=8.90  rise=3.39 twist=31.9

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 3  glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major nts=4 GGGG B.DG1011,B.DG1017,B.DG1024,B.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.DG1012,B.DG1016,B.DG1025,B.DG1007
  step#3  pm(>>,forward)  area=13.65 rise=3.49 twist=24.9

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

 1  glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1010,C.DG1018,C.DG1023,C.DG1005
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1011,C.DG1017,C.DG1024,C.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1012,C.DG1016,C.DG1025,C.DG1007
  step#1  mm(<>,outward)  area=14.87 rise=3.48 twist=16.5
  step#2  pm(>>,forward)  area=9.27  rise=3.41 twist=32.4
  step#3  pm(>>,forward)  area=14.51 rise=3.49 twist=24.3
  strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG C.DG1001,C.DG1010,C.DG1011,C.DG1012
  strand#2 DNA glyco-bond=-sss sugar=.--- nts=4 GGGG C.DG1019,C.DG1018,C.DG1017,C.DG1016
  strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG C.DG1022,C.DG1023,C.DG1024,C.DG1025
  strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG C.DG1004,C.DG1005,C.DG1006,C.DG1007

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3 stacking diagrams 
 1  glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC nts=4 GGGG C.DG1001,C.DG1019,C.DG1022,C.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1010,C.DG1018,C.DG1023,C.DG1005
  step#1  mm(<>,outward)  area=14.87 rise=3.48 twist=16.5

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1010,C.DG1018,C.DG1023,C.DG1005
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1011,C.DG1017,C.DG1024,C.DG1006
  step#2  pm(>>,forward)  area=9.27  rise=3.41 twist=32.4

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 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1011,C.DG1017,C.DG1024,C.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG C.DG1012,C.DG1016,C.DG1025,C.DG1007
  step#3  pm(>>,forward)  area=14.51 rise=3.49 twist=24.3

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

 1  glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1010,D.DG1018,D.DG1023,D.DG1005
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1011,D.DG1017,D.DG1024,D.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1012,D.DG1016,D.DG1025,D.DG1007
  step#1  mm(<>,outward)  area=15.06 rise=3.46 twist=16.1
  step#2  pm(>>,forward)  area=9.40  rise=3.41 twist=31.7
  step#3  pm(>>,forward)  area=14.51 rise=3.48 twist=24.4
  strand#1 DNA glyco-bond=s--- sugar=3--- nts=4 GGGG D.DG1001,D.DG1010,D.DG1011,D.DG1012
  strand#2 DNA glyco-bond=-sss sugar=.--- nts=4 GGGG D.DG1019,D.DG1018,D.DG1017,D.DG1016
  strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG D.DG1022,D.DG1023,D.DG1024,D.DG1025
  strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG D.DG1004,D.DG1005,D.DG1006,D.DG1007

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3 stacking diagrams 
 1  glyco-bond=s-ss sugar=3.-- groove=wn-- Major-->WC nts=4 GGGG D.DG1001,D.DG1019,D.DG1022,D.DG1004
 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1010,D.DG1018,D.DG1023,D.DG1005
  step#1  mm(<>,outward)  area=15.06 rise=3.46 twist=16.1

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 2  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1010,D.DG1018,D.DG1023,D.DG1005
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1011,D.DG1017,D.DG1024,D.DG1006
  step#2  pm(>>,forward)  area=9.40  rise=3.41 twist=31.7

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 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1011,D.DG1017,D.DG1024,D.DG1006
 4  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG D.DG1012,D.DG1016,D.DG1025,D.DG1007
  step#3  pm(>>,forward)  area=14.51 rise=3.48 twist=24.4

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List of 4 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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG1005,A.DG1010,A.DG1018,A.DG1023
 2  glyco-bond=--s- sugar=---. groove=-wn- WC-->Major nts=4 GGGG A.DG1006,A.DG1011,A.DG1017,A.DG1024
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG A.DG1007,A.DG1012,A.DG1016,A.DG1025
  step#1  pm(>>,forward)  area=9.63  rise=3.43 twist=31.8
  step#2  pm(>>,forward)  area=14.07 rise=3.47 twist=24.5
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG1005,A.DG1006,A.DG1007
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG1010,A.DG1011,A.DG1012
  strand#3  D DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG1018,A.DG1017,A.DG1016
  strand#4  U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG1023,A.DG1024,A.DG1025
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT1008,A.DT1009
  loop#2 type=lateral   strands=[#2,#3] nts=3 GTT A.DG1013,A.DT1014,A.DT1015
  loop#3 type=lateral   strands=[#3,#4] nts=4 GTTG A.DG1019,A.DT1020,A.DT1021,A.DG1022

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Stem#2, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG B.DG1005,B.DG1010,B.DG1018,B.DG1023
 2  glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major nts=4 GGGG B.DG1006,B.DG1011,B.DG1017,B.DG1024
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG B.DG1007,B.DG1012,B.DG1016,B.DG1025
  step#1  pm(>>,forward)  area=8.90  rise=3.39 twist=31.9
  step#2  pm(>>,forward)  area=13.65 rise=3.49 twist=24.9
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG1005,B.DG1006,B.DG1007
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG1010,B.DG1011,B.DG1012
  strand#3  D DNA glyco-bond=sss sugar=--- nts=3 GGG B.DG1018,B.DG1017,B.DG1016
  strand#4  U DNA glyco-bond=--- sugar=-3- nts=3 GGG B.DG1023,B.DG1024,B.DG1025
  loop#1 type=propeller strands=[#1,#2] nts=2 TT B.DT1008,B.DT1009
  loop#2 type=lateral   strands=[#2,#3] nts=3 GTT B.DG1013,B.DT1014,B.DT1015
  loop#3 type=lateral   strands=[#3,#4] nts=4 GTTG B.DG1019,B.DT1020,B.DT1021,B.DG1022

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Stem#3, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG1005,C.DG1010,C.DG1018,C.DG1023
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG1006,C.DG1011,C.DG1017,C.DG1024
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG C.DG1007,C.DG1012,C.DG1016,C.DG1025
  step#1  pm(>>,forward)  area=9.27  rise=3.41 twist=32.4
  step#2  pm(>>,forward)  area=14.51 rise=3.49 twist=24.3
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1005,C.DG1006,C.DG1007
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1010,C.DG1011,C.DG1012
  strand#3  D DNA glyco-bond=sss sugar=--- nts=3 GGG C.DG1018,C.DG1017,C.DG1016
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG C.DG1023,C.DG1024,C.DG1025
  loop#1 type=propeller strands=[#1,#2] nts=2 TT C.DT1008,C.DT1009
  loop#2 type=lateral   strands=[#2,#3] nts=3 GTT C.DG1013,C.DT1014,C.DT1015
  loop#3 type=lateral   strands=[#3,#4] nts=4 GTTG C.DG1019,C.DT1020,C.DT1021,C.DG1022

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Stem#4, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)

 1  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG D.DG1005,D.DG1010,D.DG1018,D.DG1023
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG D.DG1006,D.DG1011,D.DG1017,D.DG1024
 3  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major nts=4 GGGG D.DG1007,D.DG1012,D.DG1016,D.DG1025
  step#1  pm(>>,forward)  area=9.40  rise=3.41 twist=31.7
  step#2  pm(>>,forward)  area=14.51 rise=3.48 twist=24.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1005,D.DG1006,D.DG1007
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1010,D.DG1011,D.DG1012
  strand#3  D DNA glyco-bond=sss sugar=--- nts=3 GGG D.DG1018,D.DG1017,D.DG1016
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG1023,D.DG1024,D.DG1025
  loop#1 type=propeller strands=[#1,#2] nts=2 TT D.DT1008,D.DT1009
  loop#2 type=lateral   strands=[#2,#3] nts=3 GTT D.DG1013,D.DT1014,D.DT1015
  loop#3 type=lateral   strands=[#3,#4] nts=4 GTTG D.DG1019,D.DT1020,D.DT1021,D.DG1022

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List of 8 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=4 GTTG A.DG1001,A.DT1002,A.DT1003,A.DG1004
 2 type=lateral   helix=#1 nts=4 GTTG A.DG1019,A.DT1020,A.DT1021,A.DG1022
 3 type=lateral   helix=#2 nts=4 GTTG B.DG1001,B.DT1002,B.DT1003,B.DG1004
 4 type=lateral   helix=#2 nts=4 GTTG B.DG1019,B.DT1020,B.DT1021,B.DG1022
 5 type=lateral   helix=#3 nts=4 GTTG C.DG1001,C.DT1002,C.DT1003,C.DG1004
 6 type=lateral   helix=#3 nts=4 GTTG C.DG1019,C.DT1020,C.DT1021,C.DG1022
 7 type=lateral   helix=#4 nts=4 GTTG D.DG1001,D.DT1002,D.DT1003,D.DG1004
 8 type=lateral   helix=#4 nts=4 GTTG D.DG1019,D.DT1020,D.DT1021,D.DG1022