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

©Jiří Černý & Bohdan Schneider

Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide

Results of the assignment of 43 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
011yrj_A_U1_U2NANNANT01.30OP05
021yrj_A_U2_G3NANNANT00.55OP13
031yrj_A_G3_C4AAAAA08560.30AA08
041yrj_A_C4_G5AAwAA01650.14AA01
051yrj_A_G5_U6AAAAA00450.30AA00
061yrj_A_U6_C7AAAAA08690.26AA08
071yrj_A_C7_A8AAAAA00620.23AA00
081yrj_A_A8_C9AAAAA04360.40AA04
091yrj_A_C9_A10AAAAA00700.18AA00
101yrj_A_A10_C11AAAAA00860.29AA00
111yrj_A_C11_C12AAwAA01390.29AA01
121yrj_A_C12_G13AAAAA08640.28AA08
131yrj_A_G13_G14AAAAA00680.26AA00
141yrj_A_G14_U15AAAAA00850.19AA00
151yrj_A_U15_G16AAAAA00940.12AA00
161yrj_A_G16_A17NANNANT01.91IC02
171yrj_A_A17_A18NANNANT00.52AA02
181yrj_A_A18_G19NANNANT00.65OP12
191yrj_A_G19_U20AAAAA00500.32AA00
201yrj_A_U20_C21AAAAA00930.10AA00
211yrj_A_C21_G22AAAAA00840.15AA00
221yrj_A_G22_C23AAAAA00520.34AA00
231yrj_B_U25_G26NANNANT01.44OP16
241yrj_B_G26_C27AAAAA00610.34AA00
251yrj_B_C27_G28AAwAA01830.18AA01
261yrj_B_G28_U29NANNANT00.54AA03
271yrj_B_U29_C30AAwAA01530.33AA01
281yrj_B_C30_A31AAAAA08580.30AA08
291yrj_B_A31_C32AAAAA00640.27AA00
301yrj_B_C32_A33AAAAA00760.20AA00
311yrj_B_A33_C34AAAAA00850.17AA00
321yrj_B_C34_C35AAAAA00650.15AA00
331yrj_B_C35_G36AAAAA00690.17AA00
341yrj_B_G36_G37AAAAA03800.31AA03
351yrj_B_G37_U38AAAAA00650.21AA00
361yrj_B_U38_G39AAAAA00690.20AA00
371yrj_B_G39_A40NANNANT01.25OP03
381yrj_B_A40_A41NANNANT00.70IC03
391yrj_B_A41_G42NANNANT00.56OP11
401yrj_B_G42_U43AAAAA00410.36AA00
411yrj_B_U43_C44AAAAA08210.48AA08
421yrj_B_C44_G45NANNANT00.55AB02
431yrj_B_G45_C46AAwAA10690.23AA10

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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