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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER

Results of the assignment of 136 detected steps in 1 model(s), can be also downloaded as csv 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
0011ddy_A_G1_G2AA1AA01430.32AA01
0021ddy_A_G2_A3AAAAA08840.26AA08
0031ddy_A_A3_A4NANNANT00.70AA10
0041ddy_A_A4_C5AA1AA06170.58AA06
0051ddy_A_C5_C6AAAAA00660.22AA00
0061ddy_A_C6_G7AAAAA00210.32AA00
0071ddy_A_G7_G8AAAAA00670.23AA00
0081ddy_A_G8_U9AAAAA00670.22AA00
0091ddy_A_U9_G10NANNANT00.42IC02
0101ddy_A_G10_C11NANNANT00.73AA10
0111ddy_A_C11_G12NANNANT01.14OP04
0121ddy_A_G12_C13NANNANT00.71AB02
0131ddy_A_C13_A14NANNANT00.38ZZ01
0141ddy_A_A14_U15NANNANT00.78IC05
0151ddy_A_U15_A16NANNANT01.24ZZ1S
0161ddy_A_A16_A17AAAAA08540.38AA08
0171ddy_A_A17_C18AAAAA00650.28AA00
0181ddy_A_C18_C19AAAAA00490.33AA00
0191ddy_A_C19_A20AAAAA00800.24AA00
0201ddy_A_A20_C21AA1AA06740.26AA06
0211ddy_A_C21_C22NANNANT00.63AA03
0221ddy_A_C22_U23NANNANT00.54OP10
0231ddy_A_U23_C24NANNANT01.75OP09
0241ddy_A_C24_A25OPNOP11680.44OP11
0251ddy_A_A25_G26NANNANT01.45IC01
0261ddy_A_G26_U27NANNANT00.81BB08
0271ddy_A_U27_G28NANNANT00.85OP10
0281ddy_A_G28_C29AAAAA00570.31AA00
0291ddy_A_C29_G30ZZZZZ01280.26ZZ01
0301ddy_A_G30_A31NANNANT01.22BA16
0311ddy_A_A31_G32AA1AA01770.17AA01
0321ddy_A_G32_C33AAAAA00590.18AA00
0331ddy_A_C33_A34AAAAA00860.20AA00
0341ddy_A_A34_A35AAAAA00730.20AA00
0351ddy_C_G201_G202AA1AA01370.29AA01
0361ddy_C_G202_A203AAAAA08700.30AA08
0371ddy_C_A203_A204AAAAA00680.18AA00
0381ddy_C_A204_C205AA1AA01840.27AA01
0391ddy_C_C205_C206AAAAA08790.27AA08
0401ddy_C_C206_G207AAAAA00840.19AA00
0411ddy_C_G207_G208AAAAA00890.15AA00
0421ddy_C_G208_U209AAAAA00770.22AA00
0431ddy_C_U209_G210NANNANT00.49IC02
0441ddy_C_G210_C211NANNANT00.76AA10
0451ddy_C_C211_G212NANNANT01.21OP04
0461ddy_C_G212_C213NANNANT00.66AB02
0471ddy_C_C213_A214ZZZZZ01570.24ZZ01
0481ddy_C_A214_U215NANNANT00.76IC05
0491ddy_C_U215_A216NANNANT01.29ZZ1S
0501ddy_C_A216_A217AAAAA00300.28AA00
0511ddy_C_A217_C218AAAAA00610.27AA00
0521ddy_C_C218_C219AAAAA00220.34AA00
0531ddy_C_C219_A220AAAAA00880.22AA00
0541ddy_C_A220_C221AAAAA00810.18AA00
0551ddy_C_C221_C222A-BAB05780.20AB05
0561ddy_C_C222_U223NANNANT00.74BB07
0571ddy_C_U223_C224NANNANT00.68OP21
0581ddy_C_C224_A225NANNANT01.93OP16
0591ddy_C_A225_G226NANNANT01.24IC03
0601ddy_C_G226_U227NANNANT00.81BB08
0611ddy_C_U227_G228NANNANT00.86OP10
0621ddy_C_G228_C229AAAAA00630.28AA00
0631ddy_C_C229_G230ZZZZZ01280.28ZZ01
0641ddy_C_G230_A231NANNANT01.18BA16
0651ddy_C_A231_G232AA1AA01790.18AA01
0661ddy_C_G232_C233AAAAA08860.18AA08
0671ddy_C_C233_A234AAAAA08750.23AA08
0681ddy_C_A234_A235AAAAA00700.23AA00
0691ddy_E_G401_G402AAAAA08190.46AA08
0701ddy_E_G402_A403AA1AA01480.45AA01
0711ddy_E_A403_A404AAAAA08890.27AA08
0721ddy_E_A404_C405AA1AA01700.33AA01
0731ddy_E_C405_C406AAAAA00760.24AA00
0741ddy_E_C406_G407AAAAA00930.18AA00
0751ddy_E_G407_G408AAAAA00780.21AA00
0761ddy_E_G408_U409AAAAA00750.28AA00
0771ddy_E_U409_G410NANNANT00.52IC03
0781ddy_E_G410_C411NANNANT00.77BB13
0791ddy_E_C411_G412NANNANT01.26OP03
0801ddy_E_G412_C413NANNANT00.69AB02
0811ddy_E_C413_A414ZZZZZ01670.28ZZ01
0821ddy_E_A414_U415NANNANT00.73IC05
0831ddy_E_U415_A416NANNANT01.12OP15
0841ddy_E_A416_A417AAAAA00740.25AA00
0851ddy_E_A417_C418AAAAA00590.29AA00
0861ddy_E_C418_C419AAAAA00540.32AA00
0871ddy_E_C419_A420AAAAA00580.29AA00
0881ddy_E_A420_C421AAAAA00870.16AA00
0891ddy_E_C421_C422A-BAB05850.14AB05
0901ddy_E_C422_U423NANNANT00.71BB07
0911ddy_E_U423_C424NANNANT00.77OP21
0921ddy_E_C424_A425NANNANT00.78OP11
0931ddy_E_A425_G426NANNANT01.17IC01
0941ddy_E_G426_U427NANNANT00.82BB08
0951ddy_E_U427_G428NANNANT00.89OP10
0961ddy_E_G428_C429AAAAA00330.31AA00
0971ddy_E_C429_G430ZZZZZ01290.27ZZ01
0981ddy_E_G430_A431NANNANT01.17BA16
0991ddy_E_A431_G432AA1AA01660.22AA01
1001ddy_E_G432_C433AAAAA08780.19AA08
1011ddy_E_C433_A434AAAAA00710.24AA00
1021ddy_E_A434_A435AAAAA00600.21AA00
1031ddy_G_G601_G602AAAAA00390.32AA00
1041ddy_G_G602_A603AA1AA01650.30AA01
1051ddy_G_A603_A604NANNANT00.71BA09
1061ddy_G_A604_C605AA1AA01350.44AA01
1071ddy_G_C605_C606AAAAA00750.22AA00
1081ddy_G_C606_G607AAAAA00870.16AA00
1091ddy_G_G607_G608AAAAA00850.17AA00
1101ddy_G_G608_U609AAAAA00870.19AA00
1111ddy_G_U609_G610NANNANT00.42IC02
1121ddy_G_G610_C611NANNANT00.91OP08
1131ddy_G_C611_G612NANNANT01.18OP04
1141ddy_G_G612_C613NANNANT00.74AB02
1151ddy_G_C613_A614ZZZZZ01500.31ZZ01
1161ddy_G_A614_U615NANNANT00.77IC05
1171ddy_G_U615_A616NANNANT01.30ZZ1S
1181ddy_G_A616_A617AAAAA08710.29AA08
1191ddy_G_A617_C618AAAAA00740.23AA00
1201ddy_G_C618_C619AAAAA00180.36AA00
1211ddy_G_C619_A620AAAAA00770.24AA00
1221ddy_G_A620_C621AAAAA08930.21AA08
1231ddy_G_C621_C622A-BAB05670.12AB05
1241ddy_G_C622_U623NANNANT01.85OP19
1251ddy_G_U623_C624NANNANT01.68OP09
1261ddy_G_C624_A625NANNANT01.16OP13
1271ddy_G_A625_G626NANNANT01.46IC01
1281ddy_G_G626_U627NANNANT00.88BB08
1291ddy_G_U627_G628NANNANT01.09BB20
1301ddy_G_G628_C629AAAAA00750.23AA00
1311ddy_G_C629_G630ZZZZZ01530.24ZZ01
1321ddy_G_G630_A631NANNANT01.32BB08
1331ddy_G_A631_G632AA1AA01770.20AA01
1341ddy_G_G632_C633AAAAA08860.20AA08
1351ddy_G_C633_A634AAAAA00810.20AA00
1361ddy_G_A634_A635AAAAA00710.30AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
step:
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
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

Drag the plot for panning, scroll to zoom, click a point to show superposition in JSmol.

Download

Results (as csv)
Restraints (default edits file)
Best NtC fitted to input structure.

Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the 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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Color by NtC (balls)

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OPN

Z

N