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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION

Results of the assignment of 104 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
0011egk_A_A1_G2NANNANT00.59OP13
0021egk_A_G2_G3AAAAA00760.25AA00
0031egk_A_G3_A4AAAAA00710.18AA00
0041egk_A_A4_G5AAAAA00770.11AA00
0051egk_A_G5_A6AAAAA00790.30AA00
0061egk_A_A6_G7AAAAA00910.15AA00
0071egk_A_G7_A8AAAAA00790.15AA00
0081egk_A_A8_G9AAAAA00800.15AA00
0091egk_A_G9_A10AAAAA00710.20AA00
0101egk_A_A10_U11AAAAA00790.16AA00
0111egk_A_U11_G12AAAAA00800.23AA00
0121egk_A_G12_G13AAAAA00800.16AA00
0131egk_A_G13_G14AAAAA00910.15AA00
0141egk_A_G14_U15AAAAA00830.26AA00
0151egk_A_U15_G16AAAAA00830.21AA00
0161egk_A_G16_C17AAAAA00850.13AA00
0171egk_A_C17_G18AAAAA00770.14AA00
0181egk_A_G18_A19AAAAA00770.19AA00
0191egk_A_A19_G20AAAAA00700.28AA00
0201egk_B_DC21_DT22AAAAA00820.17AA00
0211egk_B_DT22_DC23AAAAA00910.20AA00
0221egk_B_DC23_DG24AAAAA00830.11AA00
0231egk_B_DG24_DC25AAAAA00760.14AA00
0241egk_B_DC25_DA26AAAAA00750.25AA00
0251egk_B_DA26_DC27AAAAA00910.11AA00
0261egk_B_DC27_DC28AAAAA00910.19AA00
0271egk_B_DC28_DC29AAAAA00970.09AA00
0281egk_B_DC29_DA30AAAAA00890.13AA00
0291egk_B_DA30_DG31NANNANT00.51AB03
0301egk_B_DG31_DG32NANNANT01.19OP16
0311egk_B_DG32_DC33NANNANT00.49AB04
0321egk_B_DC33_DT34BBBBB01110.28BB01
0331egk_B_DT34_DA35BBBBB00670.27BB00
0341egk_B_DA35_DG36BBBBB00310.42BB00
0351egk_B_DG36_DC37B-ABA08830.29BA08
0361egk_B_DC37_DT38AAAAA00850.23AA00
0371egk_B_DT38_DA39NANNANT00.59AB04
0381egk_B_DA39_DC40BBBBB00450.47BB00
0391egk_B_DC40_DA41NANNANT00.64BB10
0401egk_B_DA41_DA42A-BAB01420.33AB01
0411egk_B_DA42_DC43NANNANT01.81IC05
0421egk_B_DC43_DG44BBBBB00470.46BB00
0431egk_B_DG44_DA45NANNANT00.75BB04
0441egk_B_DA45_DC46NANNANT02.06OP04
0451egk_B_DC46_DT47AAAAA00700.21AA00
0461egk_B_DT47_DC48AAAAA04840.20AA04
0471egk_B_DC48_DT49AAAAA00440.34AA00
0481egk_B_DT49_DC50AAAAA00830.15AA00
0491egk_B_DC50_DT51AAAAA00900.20AA00
0501egk_B_DT51_DC52AAAAA00810.19AA00
0511egk_B_DC52_DC53AAAAA00600.23AA00
0521egk_B_DC53_DT54A-BAB05480.28AB05
0531egk_C_A101_G102NANNANT00.64OP13
0541egk_C_G102_G103AAAAA00730.15AA00
0551egk_C_G103_A104AAAAA08780.21AA08
0561egk_C_A104_G105AAAAA08870.26AA08
0571egk_C_G105_A106AAAAA00750.24AA00
0581egk_C_A106_G107AAAAA00850.16AA00
0591egk_C_G107_A108AAAAA00730.23AA00
0601egk_C_A108_G109AAAAA08790.24AA08
0611egk_C_G109_A110AAAAA08900.16AA08
0621egk_C_A110_U111AAAAA00690.17AA00
0631egk_C_U111_G112AAAAA08720.24AA08
0641egk_C_G112_G113AAAAA00830.18AA00
0651egk_C_G113_G114AAAAA00780.23AA00
0661egk_C_G114_U115AAAAA08840.21AA08
0671egk_C_U115_G116AAAAA00760.24AA00
0681egk_C_G116_C117AAAAA00690.23AA00
0691egk_C_C117_G118AAAAA08660.19AA08
0701egk_C_G118_A119AAAAA00780.26AA00
0711egk_C_A119_G120AAAAA00410.28AA00
0721egk_D_DC121_DT122AAAAA00180.33AA00
0731egk_D_DT122_DC123AAAAA00650.18AA00
0741egk_D_DC123_DG124AAAAA00660.21AA00
0751egk_D_DG124_DC125AAAAA08860.22AA08
0761egk_D_DC125_DA126AAAAA00850.26AA00
0771egk_D_DA126_DC127AAAAA00810.24AA00
0781egk_D_DC127_DC128AAAAA00900.19AA00
0791egk_D_DC128_DC129AAAAA00940.11AA00
0801egk_D_DC129_DA130AAAAA00760.20AA00
0811egk_D_DA130_DG131A-BAB01640.24AB01
0821egk_D_DG131_DG132NANNANT01.61OP13
0831egk_D_DG132_DC133A-BAB04520.25AB04
0841egk_D_DC133_DT134BBBBB01370.32BB01
0851egk_D_DT134_DA135BBBBB01310.26BB01
0861egk_D_DA135_DG136B-ABA05290.21BA05
0871egk_D_DG136_DC137BBBBB00250.30BB00
0881egk_D_DC137_DT138NANNANT00.65AB03
0891egk_D_DT138_DA139SYNAB2S90.56AB2S
0901egk_D_DA139_DC140SYNBBS1380.45BBS1
0911egk_D_DC140_DA141BBBBB00150.61BB00
0921egk_D_DA141_DA142B-ABA08630.35BA08
0931egk_D_DA142_DC143NANNANT01.17OP19
0941egk_D_DC143_DG144BBBBB00600.47BB00
0951egk_D_DG144_DA145NANNANT00.24IC05
0961egk_D_DA145_DC146NANNANT00.61OP21
0971egk_D_DC146_DT147AAAAA00640.29AA00
0981egk_D_DT147_DC148AAAAA00880.13AA00
0991egk_D_DC148_DT149AAAAA00790.22AA00
1001egk_D_DT149_DC150AAAAA00850.15AA00
1011egk_D_DC150_DT151AAAAA00620.29AA00
1021egk_D_DT151_DC152AAAAA08800.24AA08
1031egk_D_DC152_DC153AAAAA00770.23AA00
1041egk_D_DC153_DT154AAAAA09350.41AA09

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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