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(wwPDB) ID 4rd5 already assigned, checking structure ...

Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA

Results of the assignment of 56 detected steps in 1 model(s), can be also downloaded as csv file. Raw structure confal 0, percentile 0. Showing data for .

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Click a row in table or a step in JSmol for analysis of results.

Step nameCANANtCconfalrmsd
4rd5_C_DC2_DC3NANNANT00.56
4rd5_C_DC3_DT4NANNANT00.55
4rd5_C_DT4_DA5BB1BB16340.48
4rd5_C_DA5_DA6BBBBB00330.40
4rd5_C_DA6_DG7BB2BB07440.23
4rd5_C_DG7_DC8BBBBB00740.40
4rd5_C_DC8_DG9BB2BB07690.29
4rd5_C_DG9_DG10BBBBB00820.24
4rd5_C_DG10_DC11BB2BB07760.23
4rd5_C_DC11_DA12BBBBB00690.42
4rd5_C_DA12_DA13BB2BB07860.22
4rd5_C_DA13_DT14B1ABA05720.14
4rd5_C_DT14_DC15A-BAB03790.20
4rd5_C_DC15_DC16NANNANT00.50
4rd5_D_DG17_DG18AAAAA00630.21
4rd5_D_DG18_DG19A-BAB05450.21
4rd5_D_DG19_DA20NANNANT00.35
4rd5_D_DA20_DT212B1BB01490.20
4rd5_D_DT21_DT22BBBBB00490.24
4rd5_D_DT22_DG23NANNANT00.43
4rd5_D_DG23_DC24B1ABA05520.41
4rd5_D_DC24_DC252B1BB01340.34
4rd5_D_DC25_DG26BBBBB00710.28
4rd5_D_DG26_DC27BB2BB07690.21
4rd5_D_DC27_DT28BBBBB00500.35
4rd5_D_DT28_DT29BB2BB07310.52
4rd5_D_DT29_DA30BB2BB07770.21
4rd5_D_DA30_DG31miBBB10460.23
4rd5_E_DC2_DC3BB1BB17380.41
4rd5_E_DC3_DT4BBBBB00760.20
4rd5_E_DT4_DA5miBBB10450.26
4rd5_E_DA5_DA6BBBBB00680.29
4rd5_E_DA6_DG7BB2BB07530.23
4rd5_E_DG7_DC8BBBBB00400.43
4rd5_E_DC8_DG9BB2BB07700.33
4rd5_E_DG9_DG10BBBBB00830.29
4rd5_E_DG10_DC11BB2BB07620.24
4rd5_E_DC11_DA12BBBBB00650.48
4rd5_E_DA12_DA13BB2BB07240.30
4rd5_E_DA13_DT14B1ABA10740.22
4rd5_E_DT14_DC15NANNANT00.71
4rd5_E_DC15_DC16BB1BB16590.33
4rd5_F_DG17_DG18NANNANT00.48
4rd5_F_DG18_DG19NANNANT00.49
4rd5_F_DG19_DA20miBBB14280.48
4rd5_F_DA20_DT21BBBBB00380.33
4rd5_F_DT21_DT22NANNANT00.46
4rd5_F_DT22_DG23NANNANT00.38
4rd5_F_DG23_DC24B1ABA05300.45
4rd5_F_DC24_DC25A-BAB03780.35
4rd5_F_DC25_DG26BBBBB00850.23
4rd5_F_DG26_DC27BB2BB07800.24
4rd5_F_DC27_DT28BB1BB02130.38
4rd5_F_DT28_DT29BBBBB00100.48
4rd5_F_DT29_DA30B12BB04470.31
4rd5_F_DA30_DG31BB1BB02540.43

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

Download

Results (as csv)
Best NtC fitted to input structure.
Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the 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).

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA