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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 in complex with DNA containing abasic lesion

Results of the assignment of 24 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
011n48_B_DG1801_DG1802BBBBB00780.22BB00
021n48_B_DG1802_DG1803BB2BB07690.29BB07
031n48_B_DG1803_DG1804BBBBB00450.46BB00
041n48_B_DG1804_DG1805NANNANT00.40BB07
051n48_B_DG1805_DA1806BB2BB07460.41BB07
061n48_B_DA1806_DA1807BBBBB00820.25BB00
071n48_B_DA1807_DG1808B12BB04780.17BB04
081n48_B_DG1808_DG1809BBBBB00770.29BB00
091n48_B_DG1809_DA1810BBBBB00950.11BB00
101n48_B_DA1810_DC1811BBBBB00900.22BB00
111n48_B_DC1811_DT1812BBBBB00890.22BB00
121n48_C_DC1903_DA1904NANNANT00.44BB16
131n48_C_DT1906_DA1907BBBBB00420.47BB00
141n48_C_DA1907_DG1908BBBBB00890.12BB00
151n48_C_DG1908_DT1909BBBBB00920.16BB00
161n48_C_DT1909_DC1910BBBBB00730.24BB00
171n48_C_DC1910_DC1911BBBBB00790.27BB00
181n48_C_DC1911_DT1912BBBBB00800.21BB00
191n48_C_DT1912_DT1913BBBBB00690.20BB00
201n48_C_DT1913_DC1914BBBBB00730.22BB00
211n48_C_DC1914_DC1915BBBBB00790.18BB00
221n48_C_DC1915_DC1916BBBBB00660.35BB00
231n48_C_DC1916_DC1917BBBBB01770.26BB01
241n48_C_DC1917_DC1918B-ABA01130.31BA01

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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