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

©Jiří Černý & Bohdan Schneider

Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+)

Results of the assignment of 50 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
017d7w_A_G2_C3AAAAA08910.13AA08
027d7w_A_C3_U4AAAAA00940.15AA00
037d7w_A_U4_U5AAAAA00800.24AA00
047d7w_A_U5_C6AAwAA10810.23AA10
057d7w_A_C6_A7A-BAB05740.33AB05
067d7w_A_A7_A8NANNANT00.57OP26
077d7w_A_A8_C9AAAAA08470.37AA08
087d7w_A_C9_A10NANNANT00.39IC06
097d7w_A_A10_A11NANNANT00.52OP13
107d7w_A_A11_C12NANNANT01.83OP05
117d7w_A_C12_C13AAAAA00500.41AA00
127d7w_A_C13_C14AAAAA00530.37AA00
137d7w_A_C14_C15AAAAA00680.35AA00
147d7w_A_C15_G16OPNOP29370.33OP29
157d7w_A_G16_U17AAAAA00510.27AA00
167d7w_A_U17_A18AAAAA00880.15AA00
177d7w_A_A18_G19AAwAA01850.24AA01
187d7w_A_G19_G20AAAAA08880.21AA08
197d7w_A_G20_U21AAAAA08830.15AA08
207d7w_A_U21_G22AAAAA08810.21AA08
217d7w_A_G22_G23AAAAA00660.23AA00
227d7w_A_G23_G24AAwAA01620.34AA01
237d7w_A_G24_G25AAAAA08590.26AA08
247d7w_A_G25_A26AAAAA00750.18AA00
257d7w_A_A26_C27AAAAA00850.15AA00
267d7w_A_C27_G28AAAAA00710.21AA00
277d7w_A_G28_A29OPNOP03880.13OP03
287d7w_A_A29_A30AAAAA00370.38AA00
297d7w_A_A30_A31AAAAA00720.25AA00
307d7w_A_A31_G32NANNANT00.94AA08
317d7w_A_G32_U33AAAAA00870.14AA00
327d7w_A_U33_C34AAAAA00890.17AA00
337d7w_A_C34_A35AAAAA03420.22AA03
347d7w_A_A35_G36NANNANT02.71OP01
357d7w_A_G36_C37NANNANT00.67OP14
367d7w_A_C37_G38NANNANT01.00OP20
377d7w_A_G38_C39NANNANT01.15OP31
387d7w_A_C39_A40AAAAA00870.10AA00
397d7w_A_A40_C41AAAAA08820.19AA08
407d7w_A_C41_C42AAAAA00830.21AA00
417d7w_A_C42_U43AAAAA00480.12AA00
427d7w_A_U43_A44AAAAA00700.11AA00
437d7w_A_A44_C45AAwAA01640.24AA01
447d7w_A_C45_U46AAAAA08350.29AA08
457d7w_A_U46_G47AAAAA08860.19AA08
467d7w_A_G47_G48AAwAA01650.36AA01
477d7w_A_G48_A49AAAAA08930.18AA08
487d7w_A_A49_G50AAAAA00920.09AA00
497d7w_A_G50_C51AAAAA00480.23AA00
507d7w_A_C51_C52NANNANT00.49AA10

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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