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

©Jiří Černý & Bohdan Schneider

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

Results of the assignment of 54 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
012w9b_C_DG1_DG2BBBBB01340.30BB01
022w9b_C_DG2_DG3BBBBB00180.64BB00
032w9b_C_DG3_DG4BBBBB00610.27BB00
042w9b_C_DG4_DG5NANNANT00.42BB02
052w9b_C_DG5_DA6miBBB15520.43BB15
062w9b_C_DA6_DA7B12BB04190.33BB04
072w9b_C_DA7_DG8BBBBB01600.20BB01
082w9b_C_DG8_DG9BBBBB00200.45BB00
092w9b_C_DG9_DA10BBBBB00590.27BB00
102w9b_C_DA10_DT11BBBBB00660.21BB00
112w9b_C_DT11_DT12B12BB04630.22BB04
122w9b_C_DT12_DC13BBBBB00780.21BB00
132w9b_D_DG1_DG2BBBBB00490.34BB00
142w9b_D_DG2_DG3BB2BB07580.39BB07
152w9b_D_DG3_DG4NANNANT00.47BB10
162w9b_D_DG4_DG5BBBBB00450.42BB00
172w9b_D_DG5_DA6B12BB04330.36BB04
182w9b_D_DA6_DA7BBBBB00470.42BB00
192w9b_D_DA7_DG8miBBB15610.30BB15
202w9b_D_DG8_DG9BBBBB00210.37BB00
212w9b_D_DG9_DA10BBBBB00690.30BB00
222w9b_D_DA10_DT11BBBBB00520.26BB00
232w9b_D_DT11_DT12B12BB04400.18BB04
242w9b_D_DT12_DC13BBBBB01300.21BB01
252w9b_E_DA.E3_DT.E4NANNANT00.33BB16
262w9b_E_DT.E4_O2G.E5NANNANT00.42OP28
272w9b_E_O2G.E5_DG6BBBBB00180.41BB00
282w9b_E_DG6_DA7BB2BB07250.31BB07
292w9b_E_DA7_DA8miBBB15300.37BB15
302w9b_E_DA8_DT9BBBBB00540.47BB00
312w9b_E_DT9_DC10BBBBB00690.18BB00
322w9b_E_DC10_DC11BBBBB00810.21BB00
332w9b_E_DC11_DT12B12BB04130.26BB04
342w9b_E_DT12_DT13BBBBB00160.28BB00
352w9b_E_DT13_DC14BBBBB00480.33BB00
362w9b_E_DC14_DC15A-BAB03270.39AB03
372w9b_E_DC15_DC16NANNANT00.44BB04
382w9b_E_DC16_DC17BBBBB00780.21BB00
392w9b_E_DC17_DC18NANNANT00.33BA08
402w9b_F_DA.F3_DT.F4BBBBB00470.41BB00
412w9b_F_DT.F4_O2G.F5NANNANT00.74OP28
422w9b_F_O2G.F5_DG6NANNANT00.45BB10
432w9b_F_DG6_DA7NANNANT00.44BB15
442w9b_F_DA7_DA8BBwBB03240.44BB03
452w9b_F_DA8_DT9A-BAB03670.40AB03
462w9b_F_DT9_DC10B12BB05370.38BB05
472w9b_F_DC10_DC11NANNANT00.62BB10
482w9b_F_DC11_DT12NANNANT00.42BB00
492w9b_F_DT12_DT13BBBBB01190.42BB01
502w9b_F_DT13_DC14NANNANT00.43BB17
512w9b_F_DC14_DC15B12BB04370.37BB04
522w9b_F_DC15_DC16BBBBB00270.43BB00
532w9b_F_DC16_DC17BBBBB00680.27BB00
542w9b_F_DC17_DC18BB2BB07130.32BB07

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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