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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
NMR structure for Sp1 transcription factor duplex 5'-d(TGGGCGGGA)

Results of the assignment of 160 detected steps in 10 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
0016ed9-m10_A_DT1_DG2BB1BB03600.20BB03
0026ed9-m1_A_DT1_DG2BBBBB01780.27BB01
0036ed9-m2_A_DT1_DG2B-ABA05690.29BA05
0046ed9-m3_A_DT1_DG2B-ABA05760.28BA05
0056ed9-m4_A_DT1_DG2B-ABA09900.17BA09
0066ed9-m5_A_DT1_DG2B-ABA05820.26BA05
0076ed9-m6_A_DT1_DG2B-ABA05780.27BA05
0086ed9-m7_A_DT1_DG2B-ABA05830.26BA05
0096ed9-m8_A_DT1_DG2NANNANT00.77BB02
0106ed9-m9_A_DT1_DG2NANNANT00.71BB03
0116ed9-m10_A_DG2_DG3NANNANT00.74AA01
0126ed9-m1_A_DG2_DG3BB1BB03380.43BB03
0136ed9-m2_A_DG2_DG3BBBBB01420.25BB01
0146ed9-m3_A_DG2_DG3BBBBB01550.23BB01
0156ed9-m4_A_DG2_DG3A-BAB05840.13AB05
0166ed9-m5_A_DG2_DG3BBBBB01480.25BB01
0176ed9-m6_A_DG2_DG3BBBBB01360.27BB01
0186ed9-m7_A_DG2_DG3BBBBB00500.26BB00
0196ed9-m8_A_DG2_DG3BBBBB00520.42BB00
0206ed9-m9_A_DG2_DG3BBBBB00700.28BB00
0216ed9-m10_A_DG3_DG4BBBBB00430.21BB00
0226ed9-m1_A_DG3_DG4BBBBB00510.25BB00
0236ed9-m2_A_DG3_DG4BBBBB01510.23BB01
0246ed9-m3_A_DG3_DG4BBBBB00540.26BB00
0256ed9-m4_A_DG3_DG4BBBBB00600.25BB00
0266ed9-m5_A_DG3_DG4BBBBB00540.24BB00
0276ed9-m6_A_DG3_DG4BB1BB03320.41BB03
0286ed9-m7_A_DG3_DG4NANNANT00.55BA10
0296ed9-m8_A_DG3_DG4miBBB12660.25BB12
0306ed9-m9_A_DG3_DG4miBBB12730.23BB12
0316ed9-m10_A_DG4_DC5BBBBB00790.25BB00
0326ed9-m1_A_DG4_DC5BB1BB03680.29BB03
0336ed9-m2_A_DG4_DC5BB1BB03610.34BB03
0346ed9-m3_A_DG4_DC5BB1BB03440.36BB03
0356ed9-m4_A_DG4_DC5NANNANT00.45BB03
0366ed9-m5_A_DG4_DC5NANNANT00.50BA10
0376ed9-m6_A_DG4_DC5NANNANT00.77BB03
0386ed9-m7_A_DG4_DC5NANNANT00.42BB13
0396ed9-m8_A_DG4_DC5NANNANT00.86AA01
0406ed9-m9_A_DG4_DC5NANNANT00.75BB03
0416ed9-m10_A_DC5_DG6B-ABA09800.34BA09
0426ed9-m1_A_DC5_DG6miBBB12620.27BB12
0436ed9-m2_A_DC5_DG6NANNANT00.48BB12
0446ed9-m3_A_DC5_DG6B-ABA09720.37BA09
0456ed9-m4_A_DC5_DG6miBBB12760.23BB12
0466ed9-m5_A_DC5_DG6NANNANT00.69BA09
0476ed9-m6_A_DC5_DG6miBBB12710.25BB12
0486ed9-m7_A_DC5_DG6BB1BB16500.39BB16
0496ed9-m8_A_DC5_DG6A-BAB01490.27AB01
0506ed9-m9_A_DC5_DG6B-ABA05820.18BA05
0516ed9-m10_A_DG6_DG7A-BAB05390.29AB05
0526ed9-m1_A_DG6_DG7NANNANT00.96BB03
0536ed9-m2_A_DG6_DG7BB1BB16590.37BB16
0546ed9-m3_A_DG6_DG7AAAAA00260.45AA00
0556ed9-m4_A_DG6_DG7BB1BB16690.38BB16
0566ed9-m5_A_DG6_DG7A-BAB01180.41AB01
0576ed9-m6_A_DG6_DG7BB1BB16780.33BB16
0586ed9-m7_A_DG6_DG7BBBBB00650.20BB00
0596ed9-m8_A_DG6_DG7BBBBB00710.17BB00
0606ed9-m9_A_DG6_DG7A-BAB01440.36AB01
0616ed9-m10_A_DG7_DG8BB1BB03780.21BB03
0626ed9-m1_A_DG7_DG8NANNANT00.47BB08
0636ed9-m2_A_DG7_DG8BBBBB01510.24BB01
0646ed9-m3_A_DG7_DG8NANNANT00.81BA09
0656ed9-m4_A_DG7_DG8NANNANT00.55BA10
0666ed9-m5_A_DG7_DG8B-ABA10150.58BA10
0676ed9-m6_A_DG7_DG8NANNANT00.52BA10
0686ed9-m7_A_DG7_DG8NANNANT00.55BA10
0696ed9-m8_A_DG7_DG8B-ABA10140.58BA10
0706ed9-m9_A_DG7_DG8B-ABA10110.61BA10
0716ed9-m10_A_DG8_DA9BB1BB03660.30BB03
0726ed9-m1_A_DG8_DA9AAAAA00600.21AA00
0736ed9-m2_A_DG8_DA9BBBBB00480.22BB00
0746ed9-m3_A_DG8_DA9AAAAA00430.29AA00
0756ed9-m4_A_DG8_DA9AAAAA00490.39AA00
0766ed9-m5_A_DG8_DA9NANNANT00.63BB03
0776ed9-m6_A_DG8_DA9AAAAA00510.37AA00
0786ed9-m7_A_DG8_DA9AAAAA00590.34AA00
0796ed9-m8_A_DG8_DA9AAAAA00620.32AA00
0806ed9-m9_A_DG8_DA9AAAAA00580.35AA00
0816ed9-m10_B_DT10_DC11NANNANT00.82BB03
0826ed9-m1_B_DT10_DC11B-ABA05680.30BA05
0836ed9-m2_B_DT10_DC11B-ABA05870.27BA05
0846ed9-m3_B_DT10_DC11B-ABA05590.33BA05
0856ed9-m4_B_DT10_DC11B-ABA05880.29BA05
0866ed9-m5_B_DT10_DC11BBBBB00730.44BB00
0876ed9-m6_B_DT10_DC11B-ABA05860.30BA05
0886ed9-m7_B_DT10_DC11B-ABA05890.28BA05
0896ed9-m8_B_DT10_DC11B-ABA05870.29BA05
0906ed9-m9_B_DT10_DC11B-ABA05860.30BA05
0916ed9-m10_B_DC11_DC12BBBBB01520.28BB01
0926ed9-m1_B_DC11_DC12BBBBB00410.34BB00
0936ed9-m2_B_DC11_DC12BBBBB01620.23BB01
0946ed9-m3_B_DC11_DC12A-BAB01500.44AB01
0956ed9-m4_B_DC11_DC12BBBBB01190.31BB01
0966ed9-m5_B_DC11_DC12miBBB12830.26BB12
0976ed9-m6_B_DC11_DC12BBBBB01310.30BB01
0986ed9-m7_B_DC11_DC12BBBBB01470.27BB01
0996ed9-m8_B_DC11_DC12BBBBB01540.25BB01
1006ed9-m9_B_DC11_DC12BBBBB00400.33BB00
1016ed9-m10_B_DC12_DC13miBBB12690.28BB12
1026ed9-m1_B_DC12_DC13miBBB12880.23BB12
1036ed9-m2_B_DC12_DC13BB1BB03430.46BB03
1046ed9-m3_B_DC12_DC13miBBB12770.23BB12
1056ed9-m4_B_DC12_DC13miBBB12740.25BB12
1066ed9-m5_B_DC12_DC13NANNANT00.62BB13
1076ed9-m6_B_DC12_DC13miBBB12690.24BB12
1086ed9-m7_B_DC12_DC13BBBBB00470.31BB00
1096ed9-m8_B_DC12_DC13BBBBB00570.34BB00
1106ed9-m9_B_DC12_DC13miBBB12730.45BB12
1116ed9-m10_B_DC13_DG14NANNANT01.02BB13
1126ed9-m1_B_DC13_DG14NANNANT00.90BB12
1136ed9-m2_B_DC13_DG14miBBB12110.37BB12
1146ed9-m3_B_DC13_DG14NANNANT01.12BA10
1156ed9-m4_B_DC13_DG14NANNANT00.98AA01
1166ed9-m5_B_DC13_DG14NANNANT00.78BB03
1176ed9-m6_B_DC13_DG14NANNANT00.91BB03
1186ed9-m7_B_DC13_DG14miBBB12740.23BB12
1196ed9-m8_B_DC13_DG14miBBB12790.21BB12
1206ed9-m9_B_DC13_DG14NANNANT00.90BB12
1216ed9-m10_B_DG14_DC15A-BAB01130.29AB01
1226ed9-m1_B_DG14_DC15NANNANT00.80AA01
1236ed9-m2_B_DG14_DC15NANNANT00.90AA01
1246ed9-m3_B_DG14_DC15NANNANT00.52BB03
1256ed9-m4_B_DG14_DC15NANNANT00.53BB03
1266ed9-m5_B_DG14_DC15BBBBB00750.20BB00
1276ed9-m6_B_DG14_DC15B-ABA05840.15BA05
1286ed9-m7_B_DG14_DC15NANNANT00.93BB03
1296ed9-m8_B_DG14_DC15NANNANT00.83AA01
1306ed9-m9_B_DG14_DC15NANNANT00.68BB03
1316ed9-m10_B_DC15_DC16B-ABA10210.58BA10
1326ed9-m1_B_DC15_DC16NANNANT00.42AA01
1336ed9-m2_B_DC15_DC16AA1AA01780.21AA01
1346ed9-m3_B_DC15_DC16NANNANT00.78BA10
1356ed9-m4_B_DC15_DC16B-ABA10200.70BA10
1366ed9-m5_B_DC15_DC16BBBBB00720.18BB00
1376ed9-m6_B_DC15_DC16BBBBB01370.27BB01
1386ed9-m7_B_DC15_DC16NANNANT00.36BB08
1396ed9-m8_B_DC15_DC16AA1AA01840.26AA01
1406ed9-m9_B_DC15_DC16miBBB13690.35BB13
1416ed9-m10_B_DC16_DC17NANNANT00.84IC03
1426ed9-m1_B_DC16_DC17AAAAA00820.13AA00
1436ed9-m2_B_DC16_DC17NANNANT00.58BB03
1446ed9-m3_B_DC16_DC17AAAAA00800.16AA00
1456ed9-m4_B_DC16_DC17AAAAA00780.17AA00
1466ed9-m5_B_DC16_DC17B-ABA10180.59BA10
1476ed9-m6_B_DC16_DC17B-ABA10150.71BA10
1486ed9-m7_B_DC16_DC17NANNANT00.95BA10
1496ed9-m8_B_DC16_DC17NANNANT00.58BB03
1506ed9-m9_B_DC16_DC17BB1BB16460.35BB16
1516ed9-m10_B_DC17_DA18BBBBB00650.39BB00
1526ed9-m1_B_DC17_DA18AAAAA00650.23AA00
1536ed9-m2_B_DC17_DA18NANNANT01.04BA10
1546ed9-m3_B_DC17_DA18AAAAA00640.26AA00
1556ed9-m4_B_DC17_DA18AAAAA00490.30AA00
1566ed9-m5_B_DC17_DA18NANNANT00.64BB12
1576ed9-m6_B_DC17_DA18AAAAA00600.36AA00
1586ed9-m7_B_DC17_DA18AAAAA00560.33AA00
1596ed9-m8_B_DC17_DA18NANNANT01.08BA10
1606ed9-m9_B_DC17_DA18BBBBB01690.23BB01

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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IC

OPN

Z

N