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

©Jiří Černý & Bohdan Schneider

Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation

Results of the assignment of 26 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
012w8l_P_DG1_DG2miBBB10330.35BB10
022w8l_P_DG2_DG3B12BB04690.28BB04
032w8l_P_DG3_DG4BBBBB00760.31BB00
042w8l_P_DG4_DG5B12BB04490.29BB04
052w8l_P_DG5_DA6B12BB04730.19BB04
062w8l_P_DA6_DA7BBBBB00780.25BB00
072w8l_P_DA7_DG8BBBBB00340.32BB00
082w8l_P_DG8_DG9B12BB04770.20BB04
092w8l_P_DG9_DA10BBBBB00630.20BB00
102w8l_P_DA10_DT11BBBBB00900.23BB00
112w8l_P_DT11_DT12BBBBB00870.17BB00
122w8l_P_DT12_DC13BBBBB00380.43BB00
132w8l_T_DA.A3_DC.A4NANNANT01.02OP20
142w8l_T_DA.B3_DC.B4NANNANT01.15IC05
152w8l_T_DG6_DA7BBBBB00460.28BB00
162w8l_T_DA7_DA8BB2BB07230.33BB07
172w8l_T_DA8_DT9BBBBB00880.18BB00
182w8l_T_DT9_DC10BBBBB00690.16BB00
192w8l_T_DC10_DC11B12BB04430.29BB04
202w8l_T_DC11_DT12BBBBB00870.17BB00
212w8l_T_DT12_DT13BBBBB00590.28BB00
222w8l_T_DT13_DC14BBBBB00820.23BB00
232w8l_T_DC14_DC15BBBBB00830.26BB00
242w8l_T_DC15_DC16B12BB04850.17BB04
252w8l_T_DC16_DC17BBBBB00710.23BB00
262w8l_T_DC17_DC18BBBBB00680.32BB00

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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