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

©Jiří Černý & Bohdan Schneider

Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine

Results of the assignment of 28 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
012v4r_P_DG1_DG2BBBBB00890.20BB00
022v4r_P_DG2_DG3B12BB04360.33BB04
032v4r_P_DG3_DG4BBwBB02580.41BB02
042v4r_P_DG4_DG5BBBBB00540.38BB00
052v4r_P_DG5_DA6B12BB04570.34BB04
062v4r_P_DA6_DA7BBBBB00800.19BB00
072v4r_P_DA7_DG8BBBBB00760.28BB00
082v4r_P_DG8_DG9BBBBB00720.26BB00
092v4r_P_DG9_DA10BBBBB00740.25BB00
102v4r_P_DA10_DT11BBBBB00880.22BB00
112v4r_P_DT11_DT12BBBBB00780.23BB00
122v4r_P_DT12_DC13BBBBB00800.21BB00
132v4r_T_DC2_DA3NANNANT00.82AA03
142v4r_T_DA3_DC4NANNANT01.14OP22
152v4r_T_DC4_M1G5BBBBB00710.32BB00
162v4r_T_M1G5_DG6B12BB04500.39BB04
172v4r_T_DG6_DA7BBBBB00710.23BB00
182v4r_T_DA7_DA8B12BB04680.24BB04
192v4r_T_DA8_DT9BBBBB00850.21BB00
202v4r_T_DT9_DC10BBBBB00810.19BB00
212v4r_T_DC10_DC11BBBBB00540.34BB00
222v4r_T_DC11_DT12BBBBB00930.09BB00
232v4r_T_DT12_DT13BBBBB00930.14BB00
242v4r_T_DT13_DC14BBBBB00820.21BB00
252v4r_T_DC14_DC15BBBBB00760.21BB00
262v4r_T_DC15_DC16BBBBB00640.29BB00
272v4r_T_DC16_DC17BBBBB00770.29BB00
282v4r_T_DC17_DC18B12BB04620.29BB04

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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