#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
13OMJ|1|A+ 3OMJ|1|B (rep)5'-D(*CP*(C38)P*AP*GP*TP*AP*CP*TP*GP*G)-3'Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor BindingX-ray diffraction0.952010-09-08
21KGK|1|A+ 1KGK|1|B5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'Direct Observation of a Cytosine Analog that Forms Five Hydrogen Bonds to Guanosine; Guanyl G-ClampX-ray diffraction12001-12-21
31DPL|1|A+ 1DPL|1|B5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINEX-ray diffraction0.832000-04-04
43I5E|1|A5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G)-3'Allosteric Modulation of DNA by Small MoleculesX-ray diffraction0.982009-07-28
51EN8|1|ADNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')1 A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUMX-ray diffraction0.9852000-09-25
61ENE|1|ADNA (5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3')1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.X-ray diffraction0.9852000-09-25
73I5L|1|A+ 3I5L|1|B5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'Allosteric Modulation of DNA by Small MoleculesX-ray diffraction1.182009-07-28
83EY2|1|A+ 3EY2|1|B5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High ResolutionX-ray diffraction1.042009-04-28
91EN9|1|ADNA (5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3')1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.X-ray diffraction0.9852000-09-25
101EN3|1|ADNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUMX-ray diffraction0.9852000-09-25
111MLX|1|A+ 1MLX|1|B5'-D(*GP*CP*GP*TP*AP*SMTP*AP*CP*GP*C)-3'Crystal Structure Analysis of a 2'-O-[2-(Methylthio)-ethyl]-Modified Oligodeoxynucleotide DuplexX-ray diffraction1.252002-12-04
123OZ5|1|A+ 3OZ5|1|BDNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3')S-Methyl Carbocyclic LNAX-ray diffraction1.362010-11-24
132FIJ|1|A+ 2FIJ|1|B5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3'Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)X-ray diffraction1.192006-05-23
141M77|1|A5'-D(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3'Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNAX-ray diffraction1.252003-01-07
151PWF|1|A+ 1PWF|1|B5'-D(*GP*CP*GP*TP*AP*(2MU)P*(FA2)P*CP*GP*C)-3'One Sugar Pucker Fits All: Pairing Versatility Despite Conformational Uniformity in TNAX-ray diffraction1.162004-07-13
161R3G|1|A+ 1R3G|1|B5'-D(*GP*CP*GP*TP*AP*(GMU)P*AP*CP*GP*C)-3')1.16A X-ray structure of the synthetic DNA fragment with the incorporated 2'-O-[(2-Guanidinium)ethyl]-5-methyluridine residuesX-ray diffraction1.162003-10-21
171I5W|1|A+ 1I5W|1|B5'-D(*GP*CP*GP*TP*AP*(TLN)P*AP*CP*GP*C)-3'A-DNA DECAMER GCGTA(TLN)ACGCX-ray diffraction1.42001-04-04
181Y8L|1|A+ 1Y8L|1|B5'-D(*GP*CP*GP*TP*AP*(TFE)P*AP*CP*GP*C)-3')Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*)X-ray diffraction1.52005-06-28
191Y8V|1|A+ 1Y8V|1|B5'-D(*GP*CP*GP*TP*AP*(P2T)P*AP*CP*GP*C)-3'Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*)X-ray diffraction1.52005-06-28
201I0J|1|A+ 1I0J|1|B5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'1.06 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-METHYL-3'-METHYLENEPHOSPHONATE (T23) THYMINE IN PLACE OF T6, HIGH CS-SALTX-ray diffraction1.062001-04-04
211ZF1|1|A+ 1ZF1|1|B5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3'CCC A-DNAX-ray diffraction1.352005-05-10
221ZF9|1|A+ 1ZF9|1|B5'-D(*CP*CP*CP*CP*CP*GP*GP*GP*GP*G)-3'GGG Duplex A-DNAX-ray diffraction1.382005-05-10
231ZF7|1|A+ 1ZF7|1|B5'-D(*CP*CP*GP*TP*CP*GP*AP*CP*GP*G)-3'GAC Duplex B-DNAX-ray diffraction1.052005-05-10
241ZF8|1|A+ 1ZF8|1|B5'-D(*CP*CP*AP*CP*CP*GP*GP*TP*GP*G)-3'GGT Duplex A-DNAX-ray diffraction1.482005-05-10
251NVY|1|A+ 1NVY|1|Bd(TCGGTACCGA)4Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4X-ray diffraction1.52003-02-25
261ZF0|1|A+ 1ZF0|1|B5'-D(*CP*CP*GP*TP*TP*AP*AP*CP*GP*G)-3'B-DNAX-ray diffraction1.52005-05-10
271ZF5|1|A5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'GCT duplex B-DNAX-ray diffraction0.992005-05-10
281L6B|1|A+ 1L6B|1|B5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGGX-ray diffraction1.52002-08-07
291ZF6|1|A+ 1ZF6|1|B5'-D(*CP*CP*CP*CP*AP*TP*GP*GP*GP*G)-3'TGG DUPLEX A-DNAX-ray diffraction1.52005-05-10
301ZFF|1|A5'-D(*CP*CP*GP*AP*AP*TP*TP*CP*GP*G)-3'TTC Duplex B-DNAX-ray diffraction0.942005-05-10
313GGK|1|A5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'Locating monovalent cations in one turn of G/C rich B-DNAX-ray diffraction0.872010-03-09
321SK5|1|A+ 1SK5|1|B5'-D(*CP*TP*TP*TP*TP*AP*AP*AP*AP*G)-3'The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognitionX-ray diffraction0.892005-06-21
333GGI|1|A5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'Locating monovalent cations in one turn of G/C rich B-DNAX-ray diffraction0.982010-03-09
34440D|1|A+ 440D|1|BDNA (5'-D(*AP*GP*GP*GP*GP*CP*CP*CP*CP*T)-3')HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-DNA MODEL OF POLY(DG).POLY(DC)X-ray diffraction1.11999-01-15
35431D|1|A+ 431D|1|BDNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'X-ray diffraction1.151999-09-15
361XUW|1|A+ 1XUW|1|BDNA (5'-D(*GP*CP*GP*TP*AP*(NMT)P*AP*CP*GP*C)-3')Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-ray diffraction1.252004-12-14
371XUX|1|A+ 1XUX|1|BDNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-ray diffraction1.32004-12-14
381D61|1|ADNA (5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3')THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINIC FORMX-ray diffraction1.31993-04-15
393DNB|1|ADNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*TP*GP*G)-3')HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMERX-ray diffraction1.31989-01-09
401MA8|1|A+ 1MA8|1|B5'-D(*GP*CP*GP*TP*AP*UMSP*AP*CP*GP*C)-3'A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridineX-ray diffraction1.32002-12-11
411XUX|1|C+ 1XUX|1|DDNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-ray diffraction1.32004-12-14
425DNB|1|ADNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-GX-ray diffraction1.41991-10-15
431D49|1|A+ 1D49|1|BDNA (5'-D(*CP*GP*AP*TP*TP*AP*AP*TP*CP*G)-3')THE STRUCTURE OF A B-DNA DECAMER WITH A CENTRAL T-A STEP: C-G-A-T-T-A-A-T-C-GX-ray diffraction1.51992-04-15
441D23|1|A+ 1D23|1|BDNA (5'-D(*CP*GP*AP*TP*CP*GP*AP*TP*CP*G)-3')THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALSX-ray diffraction1.51991-10-15

Release history

Release0.19
Date2011-05-28

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5

#S - ordering by similarity (same as in the heat map).
#SPDBTitleMethodResolutionLengthNAKB_NA_annotationNAKB_protein_annotation
1
431D|1|A+431D|1|B
5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'X-RAY DIFFRACTION1.1510B-form double helix,double helix,structure
2
440D|1|A+440D|1|B
HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-DNA MODEL OF POLY(DG).POLY(DC)X-RAY DIFFRACTION1.110A-form double helix,double helix,structure
3
1I0J|1|A+1I0J|1|B
1.06 A STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-METHYL-3'-METHYLENEPHOSPHONATE (T23) THYMINE IN PLACE OF T6, HIGH CS-SALTX-RAY DIFFRACTION1.0610A-form double helix,double helix,structure
4
1MLX|1|A+1MLX|1|B
Crystal Structure Analysis of a 2'-O-[2-(Methylthio)-ethyl]-Modified Oligodeoxynucleotide DuplexX-RAY DIFFRACTION1.2510A-form double helix,double helix,structure
5
1Y8L|1|A+1Y8L|1|B
Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*)X-RAY DIFFRACTION1.510A-form double helix,double helix,structure
6
1XUW|1|A+1XUW|1|B
Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-RAY DIFFRACTION1.2510A-form double helix,double helix,structure
7
1Y8V|1|A+1Y8V|1|B
Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*)X-RAY DIFFRACTION1.510A-form double helix,double helix,structure
8
1PWF|1|A+1PWF|1|B
One Sugar Pucker Fits All: Pairing Versatility Despite Conformational Uniformity in TNAX-RAY DIFFRACTION1.1610double helix,structure
9
1XUX|1|C+1XUX|1|D
Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-RAY DIFFRACTION1.310A-form double helix,double helix,structure
10
1KGK|1|A+1KGK|1|B
Direct Observation of a Cytosine Analog that Forms Five Hydrogen Bonds to Guanosine; Guanyl G-ClampX-RAY DIFFRACTION110A-form double helix,double helix,structure
11
1R3G|1|A+1R3G|1|B
1.16A X-ray structure of the synthetic DNA fragment with the incorporated 2'-O-[(2-Guanidinium)ethyl]-5-methyluridine residuesX-RAY DIFFRACTION1.1610A-form double helix,double helix,structure
12
3OZ5|1|A+3OZ5|1|B
S-Methyl Carbocyclic LNAX-RAY DIFFRACTION1.3610A-form double helix,double helix,structure
13
1MA8|1|A+1MA8|1|B
A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridineX-RAY DIFFRACTION1.310A-form double helix,double helix,structure
14
1ZF6|1|A+1ZF6|1|B
TGG DUPLEX A-DNAX-RAY DIFFRACTION1.510A-form double helix,double helix,structure
15
1DPL|1|A+1DPL|1|B
A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINEX-RAY DIFFRACTION0.8310A-form double helix,double helix,structure
16
3EY2|1|A+3EY2|1|B
A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High ResolutionX-RAY DIFFRACTION1.0410A-form double helix,double helix,structure
17
1M77|1|A
Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNAX-RAY DIFFRACTION1.2510A-form double helix,double helix,structure
18
1XUX|1|A+1XUX|1|B
Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogsX-RAY DIFFRACTION1.310A-form double helix,double helix,structure
19
1I5W|1|A+1I5W|1|B
A-DNA DECAMER GCGTA(TLN)ACGCX-RAY DIFFRACTION1.410A-form double helix,double helix,structure
20
1ZF1|1|A+1ZF1|1|B
CCC A-DNAX-RAY DIFFRACTION1.3510A-form double helix,double helix,structure
21
2FIJ|1|A+2FIJ|1|B
Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)X-RAY DIFFRACTION1.1910double helix,structure
22
1ZF9|1|A+1ZF9|1|B
GGG Duplex A-DNAX-RAY DIFFRACTION1.3810A-form double helix,double helix,structure
23
1ZF8|1|A+1ZF8|1|B
GGT Duplex A-DNAX-RAY DIFFRACTION1.4810A-form double helix,double helix,structure
24
3OMJ|1|A+3OMJ|1|B
Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor BindingX-RAY DIFFRACTION0.9510B-form double helix,double helix,structure
25
3I5L|1|A+3I5L|1|B
Allosteric Modulation of DNA by Small MoleculesX-RAY DIFFRACTION1.1810B-form double helix,double helix,structure
26
3GGK|1|A
Locating monovalent cations in one turn of G/C rich B-DNAX-RAY DIFFRACTION0.8710B-form double helix,double helix,structure
27
5DNB|1|A
STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-GX-RAY DIFFRACTION1.410B-form double helix,double helix,structure
28
1D61|1|A
THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINIC FORMX-RAY DIFFRACTION1.310B-form double helix,double helix,structure
29
1EN8|1|A
1 A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUMX-RAY DIFFRACTION0.98510B-form double helix,double helix,structure
30
1ZF5|1|A
GCT duplex B-DNAX-RAY DIFFRACTION0.9910B-form double helix,double helix,structure
31
3I5E|1|A
Allosteric Modulation of DNA by Small MoleculesX-RAY DIFFRACTION0.9810B-form double helix,double helix,structure
32
1ENE|1|A
1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.X-RAY DIFFRACTION0.98510B-form double helix,double helix,structure
33
3DNB|1|A
HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMERX-RAY DIFFRACTION1.310B-form double helix,double helix,feature,mispair,structure
34
3GGI|1|A
Locating monovalent cations in one turn of G/C rich B-DNAX-RAY DIFFRACTION0.9810B-form double helix,double helix,structure
35
1EN9|1|A
1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.X-RAY DIFFRACTION0.98510B-form double helix,double helix,structure
36
1SK5|1|A+1SK5|1|B
The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognitionX-RAY DIFFRACTION0.8910B-form double helix,double helix,structure
37
1D23|1|A+1D23|1|B
THE STRUCTURE OF B-HELICAL C-G-A-T-C-G-A-T-C-G AND COMPARISON WITH C-C-A-A-C-G-T-T-G-G. THE EFFECT OF BASE PAIR REVERSALSX-RAY DIFFRACTION1.510B-form double helix,double helix,structure
38
1D49|1|A+1D49|1|B
THE STRUCTURE OF A B-DNA DECAMER WITH A CENTRAL T-A STEP: C-G-A-T-T-A-A-T-C-GX-RAY DIFFRACTION1.510B-form double helix,double helix,structure
39
1ZF7|1|A+1ZF7|1|B
GAC Duplex B-DNAX-RAY DIFFRACTION1.0510B-form double helix,double helix,structure
40
1ZF0|1|A+1ZF0|1|B
B-DNAX-RAY DIFFRACTION1.510B-form double helix,double helix,structure
41
1ZFF|1|A
TTC Duplex B-DNAX-RAY DIFFRACTION0.9410double helix,structure
42
1EN3|1|A
1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUMX-RAY DIFFRACTION0.98510B-form double helix,double helix,structure
43
1NVY|1|A+1NVY|1|B
Strontium bound to the Holliday junction sequence d(TCGGTACCGA)4X-RAY DIFFRACTION1.510Holliday junction,structure
44
1L6B|1|A+1L6B|1|B
CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGGX-RAY DIFFRACTION1.510Holliday junction,structure

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