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

©Jiří Černý & Bohdan Schneider

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct

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
012w7p_E_DG3_DG4NANNANT00.67BB02
022w7p_E_DG4_DG5NANNANT00.78BB11
032w7p_E_DG5_DA6BBBBB00400.46BB00
042w7p_E_DA6_DA7BBwBB02730.28BB02
052w7p_E_DA7_DG8BBBBB00520.29BB00
062w7p_E_DG8_DG9BBwBB02460.48BB02
072w7p_E_DG9_DA10BBBBB00390.36BB00
082w7p_E_DA10_DT11BBwBB02600.24BB02
092w7p_E_DT11_DT12BBBBB00660.29BB00
102w7p_E_DT12_DC13BBBBB00390.27BB00
112w7p_F_DC2_DA3NANNANT00.76AA06
122w7p_F_DA3_DC4NANNANT01.74IC03
132w7p_F_DC4_8OG5NANNANT01.21IC05
142w7p_F_8OG5_DG6NANNANT00.69AB02
152w7p_F_DG6_DA7NANNANT00.48BB02
162w7p_F_DA7_DA8BBBBB00870.27BB00
172w7p_F_DA8_DT9BBBBB00650.23BB00
182w7p_F_DT9_DC10B12BB04600.22BB04
192w7p_F_DC10_DC11BBBBB00670.27BB00
202w7p_F_DC11_DT12BBBBB00330.37BB00
212w7p_F_DT12_DT13BBBBB00850.17BB00
222w7p_F_DT13_DC14miBBB12870.36BB12
232w7p_F_DC14_DC15NANNANT00.91BB03
242w7p_F_DC15_DC16BBwBB11420.48BB11
252w7p_P_DG1_DG2BBBBB00370.39BB00
262w7p_P_DG2_DG3NANNANT00.47BB17
272w7p_P_DG3_DG4miBBB13340.42BB13
282w7p_P_DG4_DG5BBBBB00410.39BB00
292w7p_P_DG5_DA6BBBBB00720.31BB00
302w7p_P_DA6_DA7BBwBB02450.32BB02
312w7p_P_DA7_DG8BBBBB00760.26BB00
322w7p_P_DG8_DG9BBwBB02680.35BB02
332w7p_P_DG9_DA10BBBBB00460.36BB00
342w7p_P_DA10_DT11BBBBB00230.37BB00
352w7p_P_DT11_DT12BBBBB00690.28BB00
362w7p_P_DT12_DC13BBBBB00600.28BB00
372w7p_T_DC2_DA3NANNANT00.85BB13
382w7p_T_DA3_DC4NANNANT00.81OP28
392w7p_T_DC4_8OG5NANNANT00.79OP10
402w7p_T_8OG5_DG6SYNBBS1410.34BBS1
412w7p_T_DG6_DA7BBBBB00910.17BB00
422w7p_T_DA7_DA8BBwBB02880.25BB02
432w7p_T_DA8_DT9BBBBB00730.28BB00
442w7p_T_DT9_DC10B12BB04660.27BB04
452w7p_T_DC10_DC11BBBBB00770.29BB00
462w7p_T_DC11_DT12BBBBB00750.25BB00
472w7p_T_DT12_DT13NANNANT00.48BB02
482w7p_T_DT13_DC14BBwBB02300.42BB02
492w7p_T_DC14_DC15BBBBB00810.29BB00
502w7p_T_DC15_DC16BBBBB00290.39BB00
512w7p_T_DC16_DC17BBBBB00660.25BB00
522w7p_T_DC17_DC18BBwBB02480.27BB02

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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