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

©Jiří Černý & Bohdan Schneider

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP

Results of the assignment of 52 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
012w9c_C_DG1_DG2BBBBB00760.22BB00
022w9c_C_DG2_DG3BB2BB07700.14BB07
032w9c_C_DG3_DG4BBBBB00750.35BB00
042w9c_C_DG4_DG5BBwBB02340.40BB02
052w9c_C_DG5_DA6BBBBB00650.30BB00
062w9c_C_DA6_DA7BBBBB00870.19BB00
072w9c_C_DA7_DG8B12BB04700.28BB04
082w9c_C_DG8_DG9miBBB10640.44BB10
092w9c_C_DG9_DA10BBBBB00570.39BB00
102w9c_C_DA10_DT11BBBBB00850.23BB00
112w9c_C_DT11_DT12BBBBB00710.32BB00
122w9c_D_DG1_DG2miBBB10480.32BB10
132w9c_D_DG2_DG3BB2BB07730.36BB07
142w9c_D_DG3_DG4BBBBB00490.35BB00
152w9c_D_DG4_DG5BBBBB00370.45BB00
162w9c_D_DG5_DA6NANNANT00.51BB00
172w9c_D_DA6_DA7BBBBB00100.27BB00
182w9c_D_DA7_DG8BBBBB00560.24BB00
192w9c_D_DG8_DG9B12BB04440.40BB04
202w9c_D_DG9_DA10BBwBB03620.39BB03
212w9c_D_DA10_DT11BBBBB00420.40BB00
222w9c_D_DT11_DT12BBBBB00710.37BB00
232w9c_E_DA3_DC4NANNANT00.71AA02
242w9c_E_DC4_O2G5NANNANT00.46OP28
252w9c_E_O2G5_DG6BBBBB00310.43BB00
262w9c_E_DG6_DA7B12BB04830.18BB04
272w9c_E_DA7_DA8BBwBB02880.17BB02
282w9c_E_DA8_DT9BBBBB00370.40BB00
292w9c_E_DT9_DC10B12BB04780.25BB04
302w9c_E_DC10_DC11BBBBB00870.16BB00
312w9c_E_DC11_DT12B12BB04770.18BB04
322w9c_E_DT12_DT13BBBBB00750.28BB00
332w9c_E_DT13_DC14BBBBB00640.39BB00
342w9c_E_DC14_DC15BBBBB00680.27BB00
352w9c_E_DC15_DC16B12BB04570.19BB04
362w9c_E_DC16_DC17B12BB04540.45BB04
372w9c_E_DC17_DC18B12BB04800.26BB04
382w9c_F_DA3_DC4AAAAA02540.31AA02
392w9c_F_DC4_O2G5NANNANT00.46OP28
402w9c_F_O2G5_DG6BBBBB00630.33BB00
412w9c_F_DG6_DA7B-ABA08530.33BA08
422w9c_F_DA7_DA8NANNANT00.40AA10
432w9c_F_DA8_DT9NANNANT00.48AA08
442w9c_F_DT9_DC10NANNANT00.34AA01
452w9c_F_DC10_DC11NANNANT00.61AA03
462w9c_F_DC11_DT12B-ABA05530.44BA05
472w9c_F_DT12_DT13AAAAA02330.31AA02
482w9c_F_DT13_DC14AAAAA00140.43AA00
492w9c_F_DC14_DC15AAAAA00300.54AA00
502w9c_F_DC15_DC16AAAAA00160.40AA00
512w9c_F_DC16_DC17AAAAA00240.44AA00
522w9c_F_DC17_DC18AAAAA00340.40AA00

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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