Detailed DSSR results for the G-quadruplex: PDB entry 244d
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 244d
- Class
- DNA
- Method
- X-ray (1.2 Å)
- Summary
- The high-resolution crystal structure of a parallel-stranded guanine tetraplex
- Reference
- Laughlan G, Murchie AI, Norman DG, Moore MH, Moody PC, Lilley DM, Luisi B (1994): "The high-resolution crystal structure of a parallel-stranded guanine tetraplex." Science, 265, 520-524.
- Abstract
- Repeat tracts of guanine bases found in DNA and RNA can form tetraplex structures in the presence of a variety of monovalent cations. Evidence suggests that guanine tetraplexes assume important functions within chromosomal telomeres, immunoglobulin switch regions, and the human immunodeficiency virus genome. The structure of a parallel-stranded tetraplex formed by the hexanucleotide d(TG4T) and stabilized by sodium cations was determined by x-ray crystallography to 1.2 angstroms resolution. Sharply resolved sodium cations were found between and within planes of hydrogen-bonded guanine quartets, and an ordered groove hydration was observed. Distinct intra- and intermolecular stacking arrangements were adopted by the guanine quartets. Thymine bases were exclusively involved in making extensive lattice contacts.
- 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
List of 16 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.214 type=bowl nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 2 glyco-bond=---- sugar=---- groove=---- planarity=0.200 type=bowl nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 3 glyco-bond=---- sugar=---- groove=---- planarity=0.237 type=bowl nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 4 glyco-bond=---- sugar=---- groove=---- planarity=0.289 type=bowl nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 5 glyco-bond=---- sugar=333. groove=---- planarity=0.041 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52 6 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53 7 glyco-bond=---- sugar=---- groove=---- planarity=0.246 type=bowl nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54 8 glyco-bond=---- sugar=---- groove=---- planarity=0.255 type=bowl nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55 9 glyco-bond=---- sugar=3333 groove=---- planarity=0.045 type=planar nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92 10 glyco-bond=---- sugar=---- groove=---- planarity=0.228 type=bowl nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93 11 glyco-bond=---- sugar=---- groove=---- planarity=0.238 type=bowl nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94 12 glyco-bond=---- sugar=---- groove=---- planarity=0.236 type=bowl nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95 13 glyco-bond=---- sugar=---- groove=---- planarity=0.218 type=bowl nts=4 GGGG M.DG122,P.DG152,O.DG142,N.DG132 14 glyco-bond=---- sugar=---- groove=---- planarity=0.199 type=bowl nts=4 GGGG M.DG123,P.DG153,O.DG143,N.DG133 15 glyco-bond=---- sugar=---- groove=---- planarity=0.220 type=bowl nts=4 GGGG M.DG124,P.DG154,O.DG144,N.DG134 16 glyco-bond=---- sugar=---- groove=---- planarity=0.283 type=bowl nts=4 GGGG M.DG125,P.DG155,O.DG145,N.DG135
List of 2 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, 8 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 5 glyco-bond=---- sugar=.333 groove=---- Major-->WC nts=4 GGGG F.DG52,G.DG62,H.DG72,E.DG42 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG53,G.DG63,H.DG73,E.DG43 7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG54,G.DG64,H.DG74,E.DG44 8 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG55,G.DG65,H.DG75,E.DG45 step#1 mp(<<,backward) area=11.28 rise=3.45 twist=27.8 step#2 mp(<<,backward) area=11.73 rise=3.36 twist=27.2 step#3 mp(<<,backward) area=8.98 rise=3.36 twist=31.8 step#4 mm(<>,outward) area=13.29 rise=3.55 twist=17.4 step#5 pm(>>,forward) area=7.10 rise=3.51 twist=34.4 step#6 pm(>>,forward) area=10.63 rise=3.39 twist=29.1 step#7 pm(>>,forward) area=10.61 rise=3.40 twist=28.6 strand#1 DNA glyco-bond=-------- sugar=----.--- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,F.DG52,F.DG53,F.DG54,F.DG55 strand#2 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG D.DG35,D.DG34,D.DG33,D.DG32,G.DG62,G.DG63,G.DG64,G.DG65 strand#3 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG C.DG25,C.DG24,C.DG23,C.DG22,H.DG72,H.DG73,H.DG74,H.DG75 strand#4 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG B.DG15,B.DG14,B.DG13,B.DG12,E.DG42,E.DG43,E.DG44,E.DG45 |
| 7 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 |
 |
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 |
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4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 |
 |
5 glyco-bond=---- sugar=.333 groove=---- Major-->WC nts=4 GGGG F.DG52,G.DG62,H.DG72,E.DG42 |
 |
6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG53,G.DG63,H.DG73,E.DG43 |
 |
7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG F.DG54,G.DG64,H.DG74,E.DG44 |
Helix#2, 8 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92 5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG122,N.DG132,O.DG142,P.DG152 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG123,N.DG133,O.DG143,P.DG153 7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG124,N.DG134,O.DG144,P.DG154 8 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG125,N.DG135,O.DG145,P.DG155 step#1 mp(<<,backward) area=10.98 rise=3.40 twist=28.3 step#2 mp(<<,backward) area=10.85 rise=3.38 twist=29.3 step#3 mp(<<,backward) area=7.16 rise=3.52 twist=34.7 step#4 mm(<>,outward) area=13.66 rise=3.55 twist=17.1 step#5 pm(>>,forward) area=8.70 rise=3.37 twist=32.0 step#6 pm(>>,forward) area=11.83 rise=3.35 twist=27.3 step#7 pm(>>,forward) area=11.58 rise=3.45 twist=27.7 strand#1 DNA glyco-bond=-------- sugar=---3---- nts=8 GGGGGGGG I.DG85,I.DG84,I.DG83,I.DG82,M.DG122,M.DG123,M.DG124,M.DG125 strand#2 DNA glyco-bond=-------- sugar=---3---- nts=8 GGGGGGGG L.DG115,L.DG114,L.DG113,L.DG112,N.DG132,N.DG133,N.DG134,N.DG135 strand#3 DNA glyco-bond=-------- sugar=---3---- nts=8 GGGGGGGG K.DG105,K.DG104,K.DG103,K.DG102,O.DG142,O.DG143,O.DG144,O.DG145 strand#4 DNA glyco-bond=-------- sugar=---3---- nts=8 GGGGGGGG J.DG95,J.DG94,J.DG93,J.DG92,P.DG152,P.DG153,P.DG154,P.DG155 |
| 7 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94 |
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3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93 |
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4* glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92 |
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5 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG122,N.DG132,O.DG142,P.DG152 |
 |
6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG123,N.DG133,O.DG143,P.DG153 |
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7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG M.DG124,N.DG134,O.DG144,P.DG154 |
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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 step#1 pm(>>,forward) area=8.98 rise=3.36 twist=31.8 step#2 pm(>>,forward) area=11.73 rise=3.36 twist=27.2 step#3 pm(>>,forward) area=11.28 rise=3.45 twist=27.8 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG32,D.DG33,D.DG34,D.DG35 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG22,C.DG23,C.DG24,C.DG25 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG12,B.DG13,B.DG14,B.DG15 |
Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=333. groove=---- WC-->Major nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55 step#1 pm(>>,forward) area=7.10 rise=3.51 twist=34.4 step#2 pm(>>,forward) area=10.63 rise=3.39 twist=29.1 step#3 pm(>>,forward) area=10.61 rise=3.40 twist=28.6 strand#1 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG E.DG42,E.DG43,E.DG44,E.DG45 strand#2 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG H.DG72,H.DG73,H.DG74,H.DG75 strand#3 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG G.DG62,G.DG63,G.DG64,G.DG65 strand#4 U DNA glyco-bond=---- sugar=.--- nts=4 GGGG F.DG52,F.DG53,F.DG54,F.DG55 |
Stem#3, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG I.DG82,L.DG112,K.DG102,J.DG92 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG83,L.DG113,K.DG103,J.DG93 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG84,L.DG114,K.DG104,J.DG94 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG I.DG85,L.DG115,K.DG105,J.DG95 step#1 pm(>>,forward) area=7.16 rise=3.52 twist=34.7 step#2 pm(>>,forward) area=10.85 rise=3.38 twist=29.3 step#3 pm(>>,forward) area=10.98 rise=3.40 twist=28.3 strand#1 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG I.DG82,I.DG83,I.DG84,I.DG85 strand#2 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG L.DG112,L.DG113,L.DG114,L.DG115 strand#3 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG K.DG102,K.DG103,K.DG104,K.DG105 strand#4 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG J.DG92,J.DG93,J.DG94,J.DG95 |
Stem#4, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG122,P.DG152,O.DG142,N.DG132 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG123,P.DG153,O.DG143,N.DG133 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG124,P.DG154,O.DG144,N.DG134 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG M.DG125,P.DG155,O.DG145,N.DG135 step#1 pm(>>,forward) area=8.70 rise=3.37 twist=32.0 step#2 pm(>>,forward) area=11.83 rise=3.35 twist=27.3 step#3 pm(>>,forward) area=11.58 rise=3.45 twist=27.7 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG M.DG122,M.DG123,M.DG124,M.DG125 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG P.DG152,P.DG153,P.DG154,P.DG155 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG O.DG142,O.DG143,O.DG144,O.DG145 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG N.DG132,N.DG133,N.DG134,N.DG135 |
List of 2 G4 coaxial stacks
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5'] 2 G4 helix#2 contains 2 G4 stems: [#3,#4] [5'/5']