DNATCO v3.2: results

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct

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	2w7p_E_DG3_DG4	NAN	NANT	0	0.67	BB02
02	2w7p_E_DG4_DG5	NAN	NANT	0	0.78	BB11
03	2w7p_E_DG5_DA6	BBB	BB00	40	0.46	BB00
04	2w7p_E_DA6_DA7	BBw	BB02	73	0.28	BB02
05	2w7p_E_DA7_DG8	BBB	BB00	52	0.29	BB00
06	2w7p_E_DG8_DG9	BBw	BB02	46	0.48	BB02
07	2w7p_E_DG9_DA10	BBB	BB00	39	0.36	BB00
08	2w7p_E_DA10_DT11	BBw	BB02	60	0.24	BB02
09	2w7p_E_DT11_DT12	BBB	BB00	66	0.29	BB00
10	2w7p_E_DT12_DC13	BBB	BB00	39	0.27	BB00
11	2w7p_F_DC2_DA3	NAN	NANT	0	0.76	AA06
12	2w7p_F_DA3_DC4	NAN	NANT	0	1.74	IC03
13	2w7p_F_DC4_8OG5	NAN	NANT	0	1.21	IC05
14	2w7p_F_8OG5_DG6	NAN	NANT	0	0.69	AB02
15	2w7p_F_DG6_DA7	NAN	NANT	0	0.48	BB02
16	2w7p_F_DA7_DA8	BBB	BB00	87	0.27	BB00
17	2w7p_F_DA8_DT9	BBB	BB00	65	0.23	BB00
18	2w7p_F_DT9_DC10	B12	BB04	60	0.22	BB04
19	2w7p_F_DC10_DC11	BBB	BB00	67	0.27	BB00
20	2w7p_F_DC11_DT12	BBB	BB00	33	0.37	BB00
21	2w7p_F_DT12_DT13	BBB	BB00	85	0.17	BB00
22	2w7p_F_DT13_DC14	miB	BB12	87	0.36	BB12
23	2w7p_F_DC14_DC15	NAN	NANT	0	0.91	BB03
24	2w7p_F_DC15_DC16	BBw	BB11	42	0.48	BB11
25	2w7p_P_DG1_DG2	BBB	BB00	37	0.39	BB00
26	2w7p_P_DG2_DG3	NAN	NANT	0	0.47	BB17
27	2w7p_P_DG3_DG4	miB	BB13	34	0.42	BB13
28	2w7p_P_DG4_DG5	BBB	BB00	41	0.39	BB00
29	2w7p_P_DG5_DA6	BBB	BB00	72	0.31	BB00
30	2w7p_P_DA6_DA7	BBw	BB02	45	0.32	BB02
31	2w7p_P_DA7_DG8	BBB	BB00	76	0.26	BB00
32	2w7p_P_DG8_DG9	BBw	BB02	68	0.35	BB02
33	2w7p_P_DG9_DA10	BBB	BB00	46	0.36	BB00
34	2w7p_P_DA10_DT11	BBB	BB00	23	0.37	BB00
35	2w7p_P_DT11_DT12	BBB	BB00	69	0.28	BB00
36	2w7p_P_DT12_DC13	BBB	BB00	60	0.28	BB00
37	2w7p_T_DC2_DA3	NAN	NANT	0	0.85	BB13
38	2w7p_T_DA3_DC4	NAN	NANT	0	0.81	OP28
39	2w7p_T_DC4_8OG5	NAN	NANT	0	0.79	OP10
40	2w7p_T_8OG5_DG6	SYN	BBS1	41	0.34	BBS1
41	2w7p_T_DG6_DA7	BBB	BB00	91	0.17	BB00
42	2w7p_T_DA7_DA8	BBw	BB02	88	0.25	BB02
43	2w7p_T_DA8_DT9	BBB	BB00	73	0.28	BB00
44	2w7p_T_DT9_DC10	B12	BB04	66	0.27	BB04
45	2w7p_T_DC10_DC11	BBB	BB00	77	0.29	BB00
46	2w7p_T_DC11_DT12	BBB	BB00	75	0.25	BB00
47	2w7p_T_DT12_DT13	NAN	NANT	0	0.48	BB02
48	2w7p_T_DT13_DC14	BBw	BB02	30	0.42	BB02
49	2w7p_T_DC14_DC15	BBB	BB00	81	0.29	BB00
50	2w7p_T_DC15_DC16	BBB	BB00	29	0.39	BB00
51	2w7p_T_DC16_DC17	BBB	BB00	66	0.25	BB00
52	2w7p_T_DC17_DC18	BBw	BB02	48	0.27	BB02

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).

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Z

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