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

©Jiří Černý & Bohdan Schneider

Ternary complex of gamma-OHPDG adduct modified dna with dna (-1 primer) polymerase iv and incoming dgtp

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
014jv1_B_DC604_HN1605NANNANT00.41BB10
024jv1_B_HN1605_DG606A-BAB03220.61AB03
034jv1_B_DG606_DA607B-ABA05630.22BA05
044jv1_B_DA607_DA608NANNANT00.53BB00
054jv1_B_DA608_DT609BBBBB01770.18BB01
064jv1_B_DT609_DC610B-ABA05120.29BA05
074jv1_B_DC610_DC611BBBBB01370.29BB01
084jv1_B_DC611_DT612BBBBB01780.14BB01
094jv1_B_DT612_DT613BBBBB01930.15BB01
104jv1_B_DT613_DC614BBBBB00190.27BB00
114jv1_B_DC614_DC615B-ABA05390.25BA05
124jv1_B_DC615_DC616A-BAB03800.34AB03
134jv1_B_DC616_DC617BBBBB00820.28BB00
144jv1_B_DC617_DC618B12BB04710.23BB04
154jv1_C_DG501_DG502BBBBB00750.22BB00
164jv1_C_DG502_DG503B12BB04450.21BB04
174jv1_C_DG503_DG504BBBBB00340.30BB00
184jv1_C_DG504_DG505BBBBB00420.24BB00
194jv1_C_DG505_DA506BBBBB00160.32BB00
204jv1_C_DA506_DA507BBBBB00380.19BB00
214jv1_C_DA507_DG508BBBBB00770.23BB00
224jv1_C_DG508_DG509BBwBB02690.29BB02
234jv1_C_DG509_DA510BBBBB00490.25BB00
244jv1_C_DA510_DT511B-ABA05790.12BA05
254jv1_C_DT511_DT512BBBBB01130.28BB01
264jv1_C_DT512_DC513A-BAB01220.27AB01

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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