Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Results of the assignment of 35 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
| step number | Step name | CANA | NtC | confal | rmsd |
|---|---|---|---|---|---|
| 01 | 2oq4_C_DG402_DC403 | NAN | NANT | 0 | 0.88 |
| 02 | 2oq4_C_DC403_DT404 | BBB | BB00 | 57 | 0.32 |
| 03 | 2oq4_C_DT404_DT405 | BBB | BB00 | 59 | 0.32 |
| 04 | 2oq4_C_DT405_DC406 | B12 | BB04 | 84 | 0.13 |
| 05 | 2oq4_C_DC406_DA407 | NAN | NANT | 0 | 0.51 |
| 06 | 2oq4_C_DA407_DT408 | NAN | NANT | 0 | 0.45 |
| 07 | 2oq4_C_DT408_DC409 | BBB | BB00 | 69 | 0.29 |
| 08 | 2oq4_C_DC409_DC410 | B12 | BB04 | 83 | 0.17 |
| 09 | 2oq4_C_DC410_DT411 | BBw | BB11 | 37 | 0.43 |
| 10 | 2oq4_C_DT411_DG412 | NAN | NANT | 0 | 1.22 |
| 11 | 2oq4_D_DC422_DA423 | BB2 | BB08 | 33 | 0.35 |
| 12 | 2oq4_D_DA423_DG424 | BBB | BB00 | 57 | 0.35 |
| 13 | 2oq4_D_DG424_DG425 | NAN | NANT | 0 | 0.44 |
| 14 | 2oq4_D_DG425_DA426 | NAN | NANT | 0 | 0.52 |
| 15 | 2oq4_D_DG428_DA429 | BBw | BB02 | 91 | 0.20 |
| 16 | 2oq4_D_DA429_DA430 | BBB | BB00 | 63 | 0.34 |
| 17 | 2oq4_D_DA430_DG431 | BBB | BB00 | 61 | 0.37 |
| 18 | 2oq4_D_DG431_DC432 | BBw | BB03 | 70 | 0.21 |
| 19 | 2oq4_D_DC432_DC433 | NAN | NANT | 0 | 0.54 |
| 20 | 2oq4_E_DT404_DT405 | BBw | BB11 | 42 | 0.27 |
| 21 | 2oq4_E_DT405_DC406 | BBB | BB00 | 36 | 0.47 |
| 22 | 2oq4_E_DC406_DA407 | BBw | BB11 | 45 | 0.34 |
| 23 | 2oq4_E_DA407_DT408 | NAN | NANT | 0 | 0.63 |
| 24 | 2oq4_E_DT408_DC409 | BBB | BB00 | 73 | 0.31 |
| 25 | 2oq4_E_DC409_DC410 | BBB | BB00 | 37 | 0.34 |
| 26 | 2oq4_E_DC410_DT411 | BBB | BB00 | 25 | 0.50 |
| 27 | 2oq4_E_DT411_DG412 | NAN | NANT | 0 | 0.61 |
| 28 | 2oq4_F_DC422_DA423 | NAN | NANT | 0 | 1.07 |
| 29 | 2oq4_F_DA423_DG424 | NAN | NANT | 0 | 0.45 |
| 30 | 2oq4_F_DG424_DG425 | BBB | BB00 | 68 | 0.26 |
| 31 | 2oq4_F_DG425_DA426 | BBB | BB00 | 83 | 0.29 |
| 32 | 2oq4_F_DG428_DA429 | BBB | BB00 | 90 | 0.19 |
| 33 | 2oq4_F_DA429_DA430 | B12 | BB04 | 92 | 0.18 |
| 34 | 2oq4_F_DA430_DG431 | B12 | BB04 | 77 | 0.16 |
| 35 | 2oq4_F_DG431_DC432 | BBw | BB11 | 71 | 0.29 |
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
|
step: Table of conformers |
| δ1 | ε1 | ζ1 | α2 | β2 | γ2 | δ2 | χ1 | χ2 | μ | NN | CC | |
| step_torsions | ||||||||||||
| ntC_average | ||||||||||||
| Δ torsions | ||||||||||||
| torsion scores |
| comments | step confal = NaN cartesian RMSD = NaN Å pseudorotation: NA details: NA |
Similarity of step to class averages
Download
Results as csv or json file.Best NtC fitted to input structure.
Restraints
Restraints file for REFMAC (steps with RMSD <= 0.5Å)Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]
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).
Browse conformers
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