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

©Jiří Černý & Bohdan Schneider

Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain

Results of the assignment of 16 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
015hnf_L_DA103_DC104BBwBB11460.55BB11
025hnf_L_DC104_DC105BBBBB00570.35BB00
035hnf_L_DC105_DC106BBBBB00900.22BB00
045hnf_L_DC106_DG107BB2BB07760.37BB07
055hnf_L_DG107_DT108B-ABA05550.30BA05
065hnf_L_DT108_DG109A-BAB01330.27AB01
075hnf_L_DG109_DG110BB2BB07800.30BB07
085hnf_L_DG110_DA111BBBBB00800.16BB00
095hnf_M_DT201_DC202BBBBB00470.23BB00
105hnf_M_DC202_DC203BBBBB00640.24BB00
115hnf_M_DC203_DA204BB2BB07860.17BB07
125hnf_M_DA204_DC205B12BB04730.31BB04
135hnf_M_DC205_DG206BBBBB00710.44BB00
145hnf_M_DG206_DG207BB2BB07850.24BB07
155hnf_M_DG207_DG208BBBBB00570.32BB00
165hnf_M_DG208_DT209BBBBB00430.27BB00

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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