DNATCO v3.2: results

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP

Results of the assignment of 52 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 JSmol for analysis of results. Click column headers to sort data.

step number	Step name	CANA	NtC	confal	rmsd
01	2w9c_C_DG1_DG2	BBB	BB00	76	0.22	BB00
02	2w9c_C_DG2_DG3	BB2	BB07	70	0.14	BB07
03	2w9c_C_DG3_DG4	BBB	BB00	75	0.35	BB00
04	2w9c_C_DG4_DG5	BBw	BB02	34	0.40	BB02
05	2w9c_C_DG5_DA6	BBB	BB00	65	0.30	BB00
06	2w9c_C_DA6_DA7	BBB	BB00	87	0.19	BB00
07	2w9c_C_DA7_DG8	B12	BB04	70	0.28	BB04
08	2w9c_C_DG8_DG9	miB	BB10	64	0.44	BB10
09	2w9c_C_DG9_DA10	BBB	BB00	57	0.39	BB00
10	2w9c_C_DA10_DT11	BBB	BB00	85	0.23	BB00
11	2w9c_C_DT11_DT12	BBB	BB00	71	0.32	BB00
12	2w9c_D_DG1_DG2	miB	BB10	48	0.32	BB10
13	2w9c_D_DG2_DG3	BB2	BB07	73	0.36	BB07
14	2w9c_D_DG3_DG4	BBB	BB00	49	0.35	BB00
15	2w9c_D_DG4_DG5	BBB	BB00	37	0.45	BB00
16	2w9c_D_DG5_DA6	NAN	NANT	0	0.51	BB00
17	2w9c_D_DA6_DA7	BBB	BB00	10	0.27	BB00
18	2w9c_D_DA7_DG8	BBB	BB00	56	0.24	BB00
19	2w9c_D_DG8_DG9	B12	BB04	44	0.40	BB04
20	2w9c_D_DG9_DA10	BBw	BB03	62	0.39	BB03
21	2w9c_D_DA10_DT11	BBB	BB00	42	0.40	BB00
22	2w9c_D_DT11_DT12	BBB	BB00	71	0.37	BB00
23	2w9c_E_DA3_DC4	NAN	NANT	0	0.71	AA02
24	2w9c_E_DC4_O2G5	NAN	NANT	0	0.46	OP28
25	2w9c_E_O2G5_DG6	BBB	BB00	31	0.43	BB00
26	2w9c_E_DG6_DA7	B12	BB04	83	0.18	BB04
27	2w9c_E_DA7_DA8	BBw	BB02	88	0.17	BB02
28	2w9c_E_DA8_DT9	BBB	BB00	37	0.40	BB00
29	2w9c_E_DT9_DC10	B12	BB04	78	0.25	BB04
30	2w9c_E_DC10_DC11	BBB	BB00	87	0.16	BB00
31	2w9c_E_DC11_DT12	B12	BB04	77	0.18	BB04
32	2w9c_E_DT12_DT13	BBB	BB00	75	0.28	BB00
33	2w9c_E_DT13_DC14	BBB	BB00	64	0.39	BB00
34	2w9c_E_DC14_DC15	BBB	BB00	68	0.27	BB00
35	2w9c_E_DC15_DC16	B12	BB04	57	0.19	BB04
36	2w9c_E_DC16_DC17	B12	BB04	54	0.45	BB04
37	2w9c_E_DC17_DC18	B12	BB04	80	0.26	BB04
38	2w9c_F_DA3_DC4	AAA	AA02	54	0.31	AA02
39	2w9c_F_DC4_O2G5	NAN	NANT	0	0.46	OP28
40	2w9c_F_O2G5_DG6	BBB	BB00	63	0.33	BB00
41	2w9c_F_DG6_DA7	B-A	BA08	53	0.33	BA08
42	2w9c_F_DA7_DA8	NAN	NANT	0	0.40	AA10
43	2w9c_F_DA8_DT9	NAN	NANT	0	0.48	AA08
44	2w9c_F_DT9_DC10	NAN	NANT	0	0.34	AA01
45	2w9c_F_DC10_DC11	NAN	NANT	0	0.61	AA03
46	2w9c_F_DC11_DT12	B-A	BA05	53	0.44	BA05
47	2w9c_F_DT12_DT13	AAA	AA02	33	0.31	AA02
48	2w9c_F_DT13_DC14	AAA	AA00	14	0.43	AA00
49	2w9c_F_DC14_DC15	AAA	AA00	30	0.54	AA00
50	2w9c_F_DC15_DC16	AAA	AA00	16	0.40	AA00
51	2w9c_F_DC16_DC17	AAA	AA00	24	0.44	AA00
52	2w9c_F_DC17_DC18	AAA	AA00	34	0.40	AA00

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.
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).

Browse conformers

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A-B

B-A

IC

OPN

Z

N

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