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

©Jiří Černý & Bohdan Schneider

Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine and dTTP

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
014tqr_P_DG1_DG2BBBBB00830.30BB00
024tqr_P_DG2_DG3BB2BB07690.34BB07
034tqr_P_DG3_DG4B-ABA05870.18BA05
044tqr_P_DG4_DG5BBBBB01790.18BB01
054tqr_P_DG5_DA6BBBBB00710.33BB00
064tqr_P_DA6_DA7BBBBB00820.20BB00
074tqr_P_DA7_DG8BBBBB00760.36BB00
084tqr_P_DG8_DG9BB2BB07780.24BB07
094tqr_P_DG9_DA10BBBBB00830.20BB00
104tqr_P_DA10_DT11B-ABA01490.17BA01
114tqr_P_DT11_DT12BBBBB01430.33BB01
124tqr_T_DT1_DC2NANNANT00.61ZZ01
134tqr_T_DC2_DA3NANNANT01.37BB1S
144tqr_T_DA3_DC4NANNANT01.50OP16
154tqr_T_DG6_DA7B12BB04860.24BB04
164tqr_T_DA7_DA8B-ABA05930.21BA05
174tqr_T_DA8_DT9BBBBB01790.18BB01
184tqr_T_DT9_DC10BBwBB02100.35BB02
194tqr_T_DC10_DC11BBBBB00210.36BB00
204tqr_T_DC11_DT12BB2BB07750.29BB07
214tqr_T_DT12_DT13BBBBB01790.13BB01
224tqr_T_DT13_DC14B-ABA05800.29BA05
234tqr_T_DC14_DC15BBBBB01620.27BB01
244tqr_T_DC15_DC16BBBBB00230.32BB00
254tqr_T_DC16_DC17BBBBB00720.38BB00
264tqr_T_DC17_DC18BB2BB07700.29BB07

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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