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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
crystal structure of glycine riboswitch, soaked in Ba2+

Results of the assignment of 172 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
0013oxj_A_GDP1_G2AAAAA00520.24AA00
0023oxj_A_G2_C3AAAAA00660.21AA00
0033oxj_A_C3_U4AAAAA08720.29AA08
0043oxj_A_U4_C5AAAAA08870.23AA08
0053oxj_A_C5_U6AAAAA08880.18AA08
0063oxj_A_U6_G7AAAAA08670.40AA08
0073oxj_A_G7_G8AAAAA00560.27AA00
0083oxj_A_G8_A9OPNOP07430.31OP07
0093oxj_A_A9_G10AAAAA00820.25AA00
0103oxj_A_G10_A11NANNANT00.33AA09
0113oxj_A_A11_G12NANNANT00.93OP03
0123oxj_A_G12_A13NANNANT02.02OP09
0133oxj_A_A13_A14OPNOP13620.61OP13
0143oxj_A_A14_C15AAAAA00960.13AA00
0153oxj_A_C15_C16AAAAA00860.23AA00
0163oxj_A_C16_G17AAAAA00610.17AA00
0173oxj_A_G17_U18NANNANT00.35OP05
0183oxj_A_U18_U19NANNANT01.14IC02
0193oxj_A_U19_U20NANNANT01.54OP02
0203oxj_A_U20_A21AAAAA08640.43AA08
0213oxj_A_A21_A22AAAAA00330.39AA00
0223oxj_A_A22_U23AAAAA00890.10AA00
0233oxj_A_U23_C24AAAAA00670.33AA00
0243oxj_A_C24_G25AAAAA00570.31AA00
0253oxj_A_G25_G26AA1AA06310.29AA06
0263oxj_A_G26_U27AAAAA08540.39AA08
0273oxj_A_U27_C28NANNANT00.45AA10
0283oxj_A_C28_G29AAAAA00810.21AA00
0293oxj_A_G29_C30AAAAA04820.15AA04
0303oxj_A_C30_C31AAAAA00470.34AA00
0313oxj_A_C31_G32SYNAB2S750.17AB2S
0323oxj_A_G32_A33NANNANT01.20OP14
0333oxj_A_A33_A34NANNANT00.91OP16
0343oxj_A_A34_G35AAAAA08370.52AA08
0353oxj_A_G35_G36AAAAA00480.40AA00
0363oxj_A_G36_A37AAAAA08910.17AA08
0373oxj_A_A37_G38AAAAA03190.39AA03
0383oxj_A_G38_C39A-BAB02210.50AB02
0393oxj_A_C39_A40NANNANT01.40OP15
0403oxj_A_A40_A41AAAAA00520.33AA00
0413oxj_A_A41_G42AAAAA08530.34AA08
0423oxj_A_G42_C43AAAAA08890.15AA08
0433oxj_A_C43_U44AAAAA00880.13AA00
0443oxj_A_U44_C45AAAAA00670.17AA00
0453oxj_A_C45_U46AAAAA00700.24AA00
0463oxj_A_U46_G47AAAAA00770.16AA00
0473oxj_A_G47_C48AAAAA00880.15AA00
0483oxj_A_C48_G49AAAAA00870.15AA00
0493oxj_A_G49_G50AA1AA06770.32AA06
0503oxj_A_G50_A51NANNANT01.20OP17
0513oxj_A_A51_A52NANNANT01.25OP11
0523oxj_A_A52_A53AAAAA08700.16AA08
0533oxj_A_A53_C54AA1AA05810.26AA05
0543oxj_A_C54_G55AAAAA08670.29AA08
0553oxj_A_G55_C56AAAAA08830.23AA08
0563oxj_A_C56_A57AAAAA00880.18AA00
0573oxj_A_A57_G58AAAAA00870.20AA00
0583oxj_A_G58_A59NANNANT00.28AA06
0593oxj_A_A59_G60AAAAA00470.22AA00
0603oxj_A_G60_U61AAAAA08980.14AA08
0613oxj_A_U61_G62AAAAA08660.30AA08
0623oxj_A_G62_A63OPNOP07460.28OP07
0633oxj_A_A63_A64AAAAA00810.26AA00
0643oxj_A_A64_A65NANNANT00.48OP04
0653oxj_A_A65_C66NANNANT01.56OP16
0663oxj_A_C66_U67AAAAA04700.37AA04
0673oxj_A_U67_C68AAAAA08840.33AA08
0683oxj_A_C68_U69A-BAB05170.54AB05
0693oxj_A_U69_C70NANNANT00.75OP10
0703oxj_A_C70_A71AAAAA08810.32AA08
0713oxj_A_A71_G72AAAAA08690.28AA08
0723oxj_A_G72_G73AAAAA08670.32AA08
0733oxj_A_G73_C74AAAAA00180.37AA00
0743oxj_A_C74_A75NANNANT01.46OP16
0753oxj_A_A75_A76AAAAA00580.28AA00
0763oxj_A_A76_A77AAAAA00520.35AA00
0773oxj_A_A77_A78AAAAA00300.35AA00
0783oxj_A_A78_G79AAAAA08770.35AA08
0793oxj_A_G79_G80AAAAA00550.32AA00
0803oxj_A_G80_A81AA2AA07830.26AA07
0813oxj_A_A81_C82AAAAA08320.58AA08
0823oxj_A_C82_A83AAAAA00850.19AA00
0833oxj_A_A83_G84AAAAA08650.40AA08
0843oxj_A_G84_A85AAAAA08850.20AA08
0853oxj_A_A85_G86AAAAA00750.14AA00
0863oxj_A_G86_U87NANNANT00.32AA10
0873oxj_A_U87_CCC88A-BAB04460.27AB04
0883oxj_B_GDP1_G2AAAAA00640.26AA00
0893oxj_B_G2_C3AAAAA08920.21AA08
0903oxj_B_C3_U4AAAAA00880.14AA00
0913oxj_B_U4_C5AAAAA00890.17AA00
0923oxj_B_C5_U6AAAAA00920.14AA00
0933oxj_B_U6_G7AAAAA00760.27AA00
0943oxj_B_G7_G8AAAAA00490.31AA00
0953oxj_B_G8_A9OPNOP07370.33OP07
0963oxj_B_A9_G10AAAAA08700.20AA08
0973oxj_B_G10_A11AAAAA09710.33AA09
0983oxj_B_A11_G12NANNANT01.74IC03
0993oxj_B_G12_A13NANNANT01.97OP09
1003oxj_B_A13_A14NANNANT01.61OP17
1013oxj_B_A14_C15AAAAA08950.13AA08
1023oxj_B_C15_C16AAAAA00780.21AA00
1033oxj_B_C16_G17AAAAA00850.13AA00
1043oxj_B_G17_U18AA2AA12760.46AA12
1053oxj_B_U18_U19NANNANT01.76OP21
1063oxj_B_U19_U20NANNANT00.45OP20
1073oxj_B_U20_A21NANNANT01.71OP18
1083oxj_B_U23_C24NANNANT01.00AA12
1093oxj_B_C24_G25AAAAA00760.20AA00
1103oxj_B_G25_G26AA1AA06890.24AA06
1113oxj_B_G26_U27AAAAA08420.39AA08
1123oxj_B_U27_C28AAAAA00900.16AA00
1133oxj_B_C28_G29AAAAA08780.26AA08
1143oxj_B_G29_C30AA1AA01860.15AA01
1153oxj_B_C30_C31AAAAA00500.31AA00
1163oxj_B_C31_G32SYNAB2S550.23AB2S
1173oxj_B_G32_A33NANNANT00.92OP18
1183oxj_B_A33_A34OPNOP16250.81OP16
1193oxj_B_A34_G35AAAAA08360.56AA08
1203oxj_B_G35_G36AAAAA08770.36AA08
1213oxj_B_G36_A37AAAAA00730.23AA00
1223oxj_B_A37_G38AAAAA00390.37AA00
1233oxj_B_G38_C39NANNANT00.47AB03
1243oxj_B_C39_A40NANNANT00.78BA08
1253oxj_B_A40_A41AAAAA00750.27AA00
1263oxj_B_A41_G42AAAAA08770.29AA08
1273oxj_B_G42_C43AAAAA08940.13AA08
1283oxj_B_C43_U44AAAAA00870.22AA00
1293oxj_B_U44_C45AAAAA00850.17AA00
1303oxj_B_C45_U46AAAAA00850.17AA00
1313oxj_B_U46_G47AAAAA00870.14AA00
1323oxj_B_G47_C48AAAAA00840.24AA00
1333oxj_B_C48_G49AAAAA00910.14AA00
1343oxj_B_G49_G50NANNANT00.42OP05
1353oxj_B_G50_A51NANNANT00.59IC06
1363oxj_B_A51_A52AAAAA02330.22AA02
1373oxj_B_A52_A53NANNANT00.75OP09
1383oxj_B_A53_C54NANNANT00.37OP12
1393oxj_B_C54_G55AAAAA00860.20AA00
1403oxj_B_G55_C56AAAAA00700.20AA00
1413oxj_B_C56_A57AAAAA08720.32AA08
1423oxj_B_A57_G58AAAAA08750.34AA08
1433oxj_B_G58_A59AAAAA00740.27AA00
1443oxj_B_A59_G60AAAAA08850.23AA08
1453oxj_B_G60_U61AAAAA00700.25AA00
1463oxj_B_U61_G62AAAAA00440.35AA00
1473oxj_B_G62_A63OPNOP07730.32OP07
1483oxj_B_A63_A64AAAAA00760.29AA00
1493oxj_B_A64_A65NANNANT00.59OP03
1503oxj_B_A65_C66NANNANT01.61OP16
1513oxj_B_C66_U67NANNANT00.42AA01
1523oxj_B_U67_C68AAAAA08220.31AA08
1533oxj_B_C68_U69A-BAB05400.53AB05
1543oxj_B_U69_C70NANNANT00.62OP15
1553oxj_B_C70_A71AAAAA00440.37AA00
1563oxj_B_A71_G72AAAAA08680.35AA08
1573oxj_B_G72_G73AAAAA00730.19AA00
1583oxj_B_G73_C74AAAAA00110.41AA00
1593oxj_B_C74_A75NANNANT01.46OP16
1603oxj_B_A75_A76AAAAA08760.27AA08
1613oxj_B_A76_A77AAAAA00510.39AA00
1623oxj_B_A77_A78AAAAA08840.19AA08
1633oxj_B_A78_G79AAAAA08760.33AA08
1643oxj_B_G79_G80AAAAA00600.31AA00
1653oxj_B_G80_A81AA2AA07790.30AA07
1663oxj_B_A81_C82AAAAA08290.58AA08
1673oxj_B_C82_A83AAAAA00930.13AA00
1683oxj_B_A83_G84AAAAA08740.35AA08
1693oxj_B_G84_A85AAAAA00850.13AA00
1703oxj_B_A85_G86AAAAA00750.11AA00
1713oxj_B_G86_U87AAAAA08860.19AA08
1723oxj_B_U87_CCC88NANNANT00.52AB03

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).

Show



Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N