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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
Transition State Stabilization by a Catalytic RNA

Results of the assignment of 218 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
0011m5p_A_G1_G2AA1AA10170.30AA10
0021m5p_A_G2_C3AAAAA00130.51AA00
0031m5p_A_C3_C4AA2AA12300.61AA12
0041m5p_A_C4_A5AAAAA00540.25AA00
0051m5p_A_A5_C6AAAAA08940.13AA08
0061m5p_A_C6_C7AAAAA00750.18AA00
0071m5p_A_C7_U8AAAAA08940.15AA08
0081m5p_A_U8_G9AAAAA00900.15AA00
0091m5p_A_G9_A10AAAAA00890.22AA00
0101m5p_A_A10_C11AAAAA00890.16AA00
0111m5p_A_C11_A12A-BAB05480.50AB05
0121m5p_M_U14_C15AAAAA00360.32AA00
0131m5p_M_C15_C16AAAAA00740.22AA00
0141m5p_M_C16_U17AAAAA00750.21AA00
0151m5p_M_U17_C18AAAAA00800.19AA00
0161m5p_M_C18_U19AAAAA00860.17AA00
0171m5p_M_U19_C20AAAAA00920.13AA00
0181m5p_M_C20_C21AAAAA00750.18AA00
0191m5p_B_G1_G2AAAAA00130.29AA00
0201m5p_B_G2_A3AAAAA00420.26AA00
0211m5p_B_A3_G4AA1AA01790.21AA01
0221m5p_B_G4_A5AAAAA00510.28AA00
0231m5p_B_A5_G6AAAAA00690.24AA00
0241m5p_B_G6_A7AAAAA08540.35AA08
0251m5p_B_A7_G8AA1AA01250.46AA01
0261m5p_B_G8_A9AA2AA07700.46AA07
0271m5p_B_A9_A10AAAAA08900.14AA08
0281m5p_B_A10_G11AAAAA08820.19AA08
0291m5p_B_G11_U12AAAAA00840.31AA00
0301m5p_B_U12_C13AAAAA00890.15AA00
0311m5p_B_C13_A14NANNANT00.58AB03
0321m5p_B_A14_A15NANNANT01.61OP17
0331m5p_B_A15_C16NANNANT00.51AA04
0341m5p_B_C16_C17AAAAA00580.39AA00
0351m5p_B_C17_A18AAAAA00860.16AA00
0361m5p_B_A18_G19AAAAA00890.18AA00
0371m5p_B_G19_A20AA1AA01410.36AA01
0381m5p_B_A20_G21AAAAA08650.39AA08
0391m5p_B_G21_A22NANNANT00.53OP08
0401m5p_B_A22_A23AAAAA08740.27AA08
0411m5p_B_A23_A24AAAAA00750.23AA00
0421m5p_B_A24_C25AAAAA00730.22AA00
0431m5p_B_C25_A26AAAAA00830.17AA00
0441m5p_B_A26_C27AAAAA00890.11AA00
0451m5p_B_C27_A28AAAAA00610.15AA00
0461m5p_B_A28_C29AAAAA00950.15AA00
0471m5p_B_C29_C30AAAAA00640.19AA00
0481m5p_B_C30_A31AAAAA00720.21AA00
0491m5p_B_A31_A32AAAAA00610.26AA00
0501m5p_B_A32_C33AA1AA01600.33AA01
0511m5p_B_C33_C34AAAAA08900.22AA08
0521m5p_B_C34_C35AAAAA00790.19AA00
0531m5p_B_C35_A36AAAAA00780.23AA00
0541m5p_B_A36_U37AAAAA00450.16AA00
0551m5p_B_U37_U38ICLIC02890.18IC02
0561m5p_B_U38_G39NANNANT01.52BB07
0571m5p_B_G39_C40NANNANT00.81IC02
0581m5p_B_C40_A41NANNANT00.62OP15
0591m5p_B_A41_C42AAAAA00940.10AA00
0601m5p_B_C42_U43NANNANT01.86OP05
0611m5p_B_U43_C44AA2AA12250.58AA12
0621m5p_B_C44_C45AAAAA00640.31AA00
0631m5p_B_C45_G46NANNANT01.49OP17
0641m5p_B_G46_G47AAAAA00660.21AA00
0651m5p_B_G47_G48AAAAA00920.15AA00
0661m5p_B_G48_U49AAAAA00660.23AA00
0671m5p_B_U49_U50AA1AA01200.29AA01
0681m5p_B_U50_G51AAAAA08940.15AA08
0691m5p_B_G51_G52AAAAA08810.29AA08
0701m5p_B_G52_U53AAAAA00790.17AA00
0711m5p_B_U53_G54AAAAA00940.12AA00
0721m5p_B_G54_G55A-BAB05670.40AB05
0731m5p_B_G55_U56NANNANT00.54OP13
0741m5p_B_U56_A57NANNANT00.82OP21
0751m5p_B_A57_U58NANNANT01.62OP09
0761m5p_B_U58_A59OPNOP11800.30OP11
0771m5p_B_A59_U60AA1AA06480.57AA06
0781m5p_B_U60_U61NANNANT01.39AA11
0791m5p_B_U61_A62NANNANT00.81AA03
0801m5p_B_A62_C63AAAAA08410.43AA08
0811m5p_B_C63_C64AAAAA00820.19AA00
0821m5p_B_C64_U65AAAAA00810.23AA00
0831m5p_B_U65_G66AA1AA01840.23AA01
0841m5p_B_G66_G67AA1AA11930.21AA11
0851m5p_B_G67_U68AAAAA00400.27AA00
0861m5p_B_U68_A69AAAAA08730.31AA08
0871m5p_B_A69_C70AA1AA01560.32AA01
0881m5p_B_C70_G71AAAAA08420.35AA08
0891m5p_B_G71_G72AAAAA00160.44AA00
0901m5p_B_G72_G73NANNANT00.65BB2S
0911m5p_B_G73_G74NANNANT00.36AAS1
0921m5p_B_G74_G75AAAAA00740.23AA00
0931m5p_B_G75_A76NANNANT02.29IC01
0941m5p_B_A76_A77SYNAAS1500.42AAS1
0951m5p_B_A77_A78AAAAA00440.27AA00
0961m5p_B_A78_C79NANNANT01.00AA08
0971m5p_B_C79_U80AAAAA00670.25AA00
0981m5p_B_U80_U81AA1AA06890.24AA06
0991m5p_B_U81_C82AA1AA06680.37AA06
1001m5p_B_C82_G83AAAAA08360.38AA08
1011m5p_B_G83_U84AA1AA06470.36AA06
1021m5p_B_U84_G85NANNANT01.40OP17
1031m5p_B_G85_G86AAAAA08410.38AA08
1041m5p_B_G86_U87AAAAA00180.38AA00
1051m5p_B_U87_G88AAAAA00790.26AA00
1061m5p_B_G88_G89AAAAA00720.22AA00
1071m5p_B_G89_C90AAAAA00940.16AA00
1081m5p_B_C90_C91AA1AA01700.27AA01
1091m5p_B_C91_G92NANNANT01.61OP17
1101m5p_D_G1_G2AA1AA06490.37AA06
1111m5p_D_G2_C3AAAAA08650.32AA08
1121m5p_D_C3_C4AAAAA08620.45AA08
1131m5p_D_C4_A5AAAAA00870.19AA00
1141m5p_D_A5_C6AAAAA08900.17AA08
1151m5p_D_C6_C7AAAAA00820.22AA00
1161m5p_D_C7_U8AAAAA00870.13AA00
1171m5p_D_U8_G9AAAAA00890.19AA00
1181m5p_D_G9_A10AAAAA00790.26AA00
1191m5p_D_A10_C11AAAAA00780.17AA00
1201m5p_D_C11_A12A-BAB05300.47AB05
1211m5p_P_U14_C15AAAAA00500.33AA00
1221m5p_P_C15_C16AA1AA01690.31AA01
1231m5p_P_C16_U17AAAAA08810.28AA08
1241m5p_P_U17_C18AAAAA08880.17AA08
1251m5p_P_C18_U19AAAAA00650.17AA00
1261m5p_P_U19_C20AAAAA00870.17AA00
1271m5p_P_C20_C21AAAAA00350.31AA00
1281m5p_E_G1_G2AAAAA0880.49AA08
1291m5p_E_G2_A3AAAAA00960.12AA00
1301m5p_E_A3_G4AAAAA00880.16AA00
1311m5p_E_G4_A5AAAAA00880.23AA00
1321m5p_E_A5_G6AA1AA01810.33AA01
1331m5p_E_G6_A7AAAAA08850.25AA08
1341m5p_E_A7_G8AAAAA00270.44AA00
1351m5p_E_G8_A9AA2AA12890.32AA12
1361m5p_E_A9_A10AAAAA08880.16AA08
1371m5p_E_A10_G11AAAAA08790.17AA08
1381m5p_E_G11_U12AAAAA00840.26AA00
1391m5p_E_U12_C13AAAAA00870.12AA00
1401m5p_E_C13_A14NANNANT00.48AB04
1411m5p_E_A14_A15NANNANT02.39OP01
1421m5p_E_A15_C16AAAAA00780.14AA00
1431m5p_E_C16_C17AAAAA00850.21AA00
1441m5p_E_C17_A18AAAAA00880.12AA00
1451m5p_E_A18_G19AAAAA00870.28AA00
1461m5p_E_G19_A20AAAAA00650.27AA00
1471m5p_E_A20_G21AAAAA00610.32AA00
1481m5p_E_G21_A22NANNANT00.51OP08
1491m5p_E_A22_A23AAAAA00380.33AA00
1501m5p_E_A23_A24AAAAA00820.22AA00
1511m5p_E_A24_C25AAAAA00750.25AA00
1521m5p_E_C25_A26AA1AA01460.29AA01
1531m5p_E_A26_C27AAAAA08830.26AA08
1541m5p_E_C27_A28AAAAA00420.25AA00
1551m5p_E_A28_C29AAAAA00810.26AA00
1561m5p_E_C29_C30AAAAA00950.10AA00
1571m5p_E_C30_A31AAAAA00910.17AA00
1581m5p_E_A31_A32AAAAA00790.23AA00
1591m5p_E_A32_C33AAAAA00740.17AA00
1601m5p_E_C33_C34AAAAA00900.16AA00
1611m5p_E_C34_C35AAAAA00820.18AA00
1621m5p_E_C35_A36AAAAA00470.23AA00
1631m5p_E_A36_U37AAAAA04790.20AA04
1641m5p_E_U37_U38ICLIC02750.14IC02
1651m5p_E_U38_G39NANNANT01.49BB07
1661m5p_E_G39_C40NANNANT00.72IC02
1671m5p_E_C40_A41NANNANT00.66OP15
1681m5p_E_A41_C42NANNANT00.46AA04
1691m5p_E_C42_U43NANNANT01.99AA01
1701m5p_E_U43_C44NANNANT01.04OP04
1711m5p_E_C44_C45AAAAA08580.22AA08
1721m5p_E_C45_G46NANNANT01.47OP17
1731m5p_E_G46_G47AAAAA00700.24AA00
1741m5p_E_G47_G48AAAAA00410.23AA00
1751m5p_E_G48_U49AAAAA00680.23AA00
1761m5p_E_U49_U50AAAAA00820.19AA00
1771m5p_E_U50_G51AAAAA00940.11AA00
1781m5p_E_G51_G52AAAAA00870.17AA00
1791m5p_E_G52_U53AAAAA00970.12AA00
1801m5p_E_U53_G54AAAAA00700.14AA00
1811m5p_E_G54_G55NANNANT00.48AB04
1821m5p_E_G55_U56NANNANT02.19OP01
1831m5p_E_U56_A57NANNANT00.84OP21
1841m5p_E_A57_U58NANNANT01.61OP09
1851m5p_E_U58_A59OPNOP11820.31OP11
1861m5p_E_A59_U60NANNANT00.42AB04
1871m5p_E_U60_U61NANNANT01.43AB04
1881m5p_E_U61_A62NANNANT01.46OP15
1891m5p_E_A62_C63AAAAA00120.51AA00
1901m5p_E_C63_C64AAAAA00930.14AA00
1911m5p_E_C64_U65AAAAA00840.17AA00
1921m5p_E_U65_G66AAAAA00740.24AA00
1931m5p_E_G66_G67AA1AA06830.20AA06
1941m5p_E_G67_U68A-BAB04530.36AB04
1951m5p_E_U68_A69NANNANT00.41BA05
1961m5p_E_A69_C70AAAAA00630.20AA00
1971m5p_E_C70_G71AAAAA00760.27AA00
1981m5p_E_G71_G72AAAAA08750.31AA08
1991m5p_E_G72_G73AA1AA01720.33AA01
2001m5p_E_G73_G74AAAAA00640.33AA00
2011m5p_E_G74_G75AAAAA08130.50AA08
2021m5p_E_G75_A76NANNANT00.93OP04
2031m5p_E_A76_A77NANNANT00.80AA03
2041m5p_E_A77_A78AA2AA12240.66AA12
2051m5p_E_A78_C79NANNANT01.59AA10
2061m5p_E_C79_U80AAAAA08810.30AA08
2071m5p_E_U80_U81AAAAA00300.43AA00
2081m5p_E_U81_C82AAAAA00900.18AA00
2091m5p_E_C82_G83AAAAA00730.29AA00
2101m5p_E_G83_U84AAAAA08640.28AA08
2111m5p_E_U84_G85NANNANT01.38OP16
2121m5p_E_G85_G86AA1AA01400.43AA01
2131m5p_E_G86_U87AA1AA0650.64AA06
2141m5p_E_U87_G88AAAAA00790.26AA00
2151m5p_E_G88_G89AAAAA00900.16AA00
2161m5p_E_G89_C90AA1AA06690.38AA06
2171m5p_E_C90_C91NANNANT01.05AA11
2181m5p_E_C91_G92AA1AA01840.18AA01

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
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Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N