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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE MOIETY

Results of the assignment of 18 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
01219d_A_DG1_DC2AAAAA00280.33AA00
02219d_A_DC2_DT3NANNANT00.72BB16
03219d_A_DT3_DA4NANNANT00.34BA05
04219d_A_DA4_DT5NANNANT00.59AB04
05219d_A_DT5_DA6BBwBB16220.55BB16
06219d_A_DA6_DA7BBBBB0170.38BB01
07219d_A_DA7_PST8NANNANT00.58BB08
08219d_A_PST8_DG9BBBBB01490.24BB01
09219d_A_DG9_DG10NANNANT00.40BA10
10219d_B_C11_C12AAAAA00720.24AA00
11219d_B_C12_A13AAwAA01610.23AA01
12219d_B_A13_U14NANNANT00.42AA08
13219d_B_U14_U15AAwAA01480.27AA01
14219d_B_U15_A16AAAAA00740.34AA00
15219d_B_A16_U17AAwAA01640.32AA01
16219d_B_U17_A18AAAAA00280.34AA00
17219d_B_A18_G19AAwAA01640.29AA01
18219d_B_G19_C20NANNANT00.54AA01

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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