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

©Jiří Černý & Bohdan Schneider

Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4

Results of the assignment of 27 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
014jv0_B_DT4_KAG5B-ABA08440.55BA08
024jv0_B_KAG5_DG6BBBBB01230.34BB01
034jv0_B_DG6_DA7BBBBB00300.40BB00
044jv0_B_DA7_DA8B-ABA08470.41BA08
054jv0_B_DA8_DT9BBBBB01450.23BB01
064jv0_B_DT9_DC10B-ABA08750.36BA08
074jv0_B_DC10_DC11A-BAB03840.38AB03
084jv0_B_DC11_DT12miBBB10780.25BB10
094jv0_B_DT12_DT13BBBBB01780.17BB01
104jv0_B_DT13_DC14B-ABA05520.25BA05
114jv0_B_DC14_DC15B-ABA0590.28BA05
124jv0_B_DC15_DC16A-BAB01140.38AB01
134jv0_B_DC16_DC17BBBBB00400.31BB00
144jv0_B_DC17_DC18NANNANT00.51BB04
154jv0_C_DG19_DG20A-BAB03320.34AB03
164jv0_C_DG20_DG21miBBB15410.42BB15
174jv0_C_DG21_DG22BBBBB00290.25BB00
184jv0_C_DG22_DG23NANNANT00.29BB05
194jv0_C_DG23_DA24NANNANT00.46BB16
204jv0_C_DA24_DA25BBBBB00490.25BB00
214jv0_C_DA25_DG26B12BB04650.31BB04
224jv0_C_DG26_DG27B12BB04110.35BB04
234jv0_C_DG27_DA28BBBBB00410.22BB00
244jv0_C_DA28_DT29BBBBB01350.26BB01
254jv0_C_DT29_DT30BBBBB01410.23BB01
264jv0_C_DT30_DC31BBBBB01630.26BB01
274jv0_C_DC31_DC32BBBBB00230.32BB00

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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