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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

CPD lesion containing RNA Polymerase II elongation complex B

Results of the assignment of 32 detected steps in 1 model(s), can be also downloaded as csv or json 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
012ja6_N_DT0_DA1NANNANT00.49BB00
022ja6_N_DA1_DA2BBBBB00290.43BB00
032ja6_N_DA2_DG3BBBBB00150.38BB00
042ja6_N_DG3_DT4BBwBB02120.52BB02
052ja6_N_DT4_DA5BBBBB00610.30BB00
062ja6_N_DA5_DC6BBBBB0070.43BB00
072ja6_N_DC6_DT7BBBBB00380.42BB00
082ja6_P_U0_U1AAAAA04320.57AA04
092ja6_P_U1_C2AAAAA00600.24AA00
102ja6_P_C2_G3AAAAA00520.24AA00
112ja6_P_G3_A4AAAAA08550.32AA08
122ja6_P_A4_C5AAAAA08440.37AA08
132ja6_P_C5_C6AAAAA08400.44AA08
142ja6_P_C6_A7AAAAA03400.29AA03
152ja6_P_A7_G8NANNANT00.57AA03
162ja6_P_G8_G9NANNANT00.76AA07
172ja6_T_DA10_DG11NANNANT00.62BB00
182ja6_T_DG11_DT12BBBBB00710.32BB00
192ja6_T_DT12_DA13BBBBB00670.29BB00
202ja6_T_DA13_DC14BBBBB00220.39BB00
212ja6_T_DC14_DT15BBBBB00120.40BB00
222ja6_T_DT15_DT16miBBB15380.32BB15
232ja6_T_DT19_DC20NANNANT00.52AA02
242ja6_T_DC20_DC21AAwAA01310.18AA01
252ja6_T_DC21_BRU22AAAAA03660.25AA03
262ja6_T_BRU22_DG23AAwAA11320.32AA11
272ja6_T_DG23_DG24NANNANT00.42AA08
282ja6_T_DG24_DT25NANNANT00.52BB17
292ja6_T_DT25_DC26NANNANT00.30BA05
302ja6_T_DC26_DA27AAAAA02170.55AA02
312ja6_T_DA27_DT28NANNANT00.38BA05
322ja6_T_DT28_DT29AAAAA02510.66AA02

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
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

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of 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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