5DNM: Base Pair Morphology Parameters

A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 31-May-2023 number of released structures: 12820

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NDB ID: 5DNM PDB ID: 5DNM

Base Pair Morphology Parameters

CSV Format

Model Number	Pair Number	Pair Name	Shear	Stretch	Stagger	Buckle	Propellor	Opening
1	1	I_DA-72:DT72_J	-1.282	-0.116	0.141	-10.088	-10.724	-8.073
1	4	I_DA-69:DT69_J	0.272	-0.115	-0.345	7.372	-7.505	5.325
1	5	I_DA-68:DT68_J	0.591	-0.041	0.209	11.193	-19.332	-0.284
1	7	I_DA-66:DT66_J	0.816	-0.043	0.525	8.863	-17.785	-4.053
1	11	I_DA-62:DT62_J	0.702	-0.363	0.984	9.085	-12.494	-9.985
1	17	I_DA-56:DT56_J	0.473	-0.139	0.741	19.456	-9.812	0.762
1	19	I_DA-54:DT54_J	0.552	-0.027	-0.367	2.438	-8.594	-3.402
1	21	I_DA-52:DT52_J	0.863	0.057	-0.585	-20.501	-15.796	-13.9
1	24	I_DA-49:DT49_J	-0.476	-0.006	0.723	-6.541	-0.962	3.349
1	27	I_DA-46:DT46_J	0.228	0.023	0.794	32.59	-25.849	-6.386
1	28	I_DA-45:DT45_J	0.937	-0.045	0.442	23.253	-33.254	-7.812
1	29	I_DA-44:DT44_J	0.103	-0.337	1.034	9.449	-32.215	-2.285
1	30	I_DA-43:DT43_J	-0.179	0.013	0.567	9.432	-16.575	-2.66
1	35	I_DA-38:DT38_J	-0.63	-0.277	0.154	-18.678	-14.805	-12.095
1	40	I_DA-32:DT32_J	-1.233	-0.151	-0.6	-3.188	-23.877	8.926
1	41	I_DA-31:DT31_J	-0.898	0.029	0.193	1.804	-13.292	1.407
1	42	I_DA-30:DT30_J	-0.623	-0.009	0.791	-0.17	2.473	2.88
1	50	I_DA-22:DT22_J	-0.009	-0.071	0.874	16.007	2.823	-4.679
1	53	I_DA-19:DT19_J	-0.59	-0.212	-0.17	1.901	-22.705	-2.223
1	54	I_DA-18:DT18_J	0.351	0.09	0.035	-2.192	-19.506	8.69
1	55	I_DA-17:DT17_J	0.467	0.066	0.201	-7.882	-16.876	-2.735
1	56	I_DA-16:DT16_J	-0.084	-0.253	0.754	-0.704	-11.209	-5.773
1	59	I_DA-12:DT12_J	-0.488	-0.302	0.767	-1.41	-2.105	-9.788
1	65	I_DA-6:DT6_J	0.6	-0.203	-0.471	-2.459	-26.623	-7.07
1	70	I_DA-1:DT1_J	-0.421	0.031	-0.109	-0.071	-16.03	2.489
1	71	I_DA0:DT0_J	0.569	-0.181	0.288	-4.282	-10.766	1.177
1	74	I_DA3:DT-3_J	-0.441	0.091	0.156	5.879	-20.797	-2.927
1	79	I_DA8:DT-8_J	0.08	-0.177	0.06	-0.474	-9.523	3.002
1	80	I_DA9:DT-9_J	-0.156	-0.137	-0.071	3.094	-15.718	4.861
1	82	I_DA11:DT-11_J	0.113	-0.183	-0.182	-1.041	-14.974	0.57
1	92	I_DA25:DT-25_J	1.469	-0.002	0.73	1.958	-22.496	-15.332
1	95	I_DA28:DT-28_J	-1.006	0.055	-0.52	-21.928	-17.227	0.651
1	102	I_DA35:DT-35_J	-0.478	0.118	0.424	1.581	-17.769	-3.447
1	103	I_DA36:DT-36_J	0.049	-0.188	0.669	9.544	-11.698	-4.22
1	104	I_DA37:DT-37_J	0.567	-0.236	0.354	12.547	-3.714	-2.58
1	106	I_DA39:DT-39_J	-0.089	-0.324	-0.921	-18.808	-6.933	-1.805
1	108	I_DA41:DT-41_J	0.342	-0.348	-0.743	-11.419	-14.263	-10.973
1	116	I_DA50:DC-51_J	-1.493	-0.216	-0.466	14.257	-28.157	-4.622
1	123	I_DA59:DT-59_J	0.514	0.461	1.098	22.577	-14.429	5.441
1	129	I_DA65:DT-65_J	-0.895	-0.13	-0.012	0.392	-13.828	-6.3
1	131	I_DA67:DT-67_J	-0.176	-0.251	0.212	-4.062	-6.428	0.993
1	135	I_DA71:DT-71_J	1.014	-0.217	-0.272	9.31	-5.554	-3.539
1	3	I_DC-70:DG70_J	-0.496	0.409	-0.045	-4.491	2.285	5.763
1	9	I_DC-64:DG64_J	0.305	-0.111	-0.012	10.858	-14.97	-0.216
1	10	I_DC-63:DG63_J	-0.728	0.327	-0.09	2.021	-21.41	1.111
1	12	I_DC-61:DG61_J	0.362	0.666	-0.138	18.003	-19.785	14.551
1	13	I_DC-60:DG60_J	0.523	0.141	-0.381	0.058	-12.616	11.951
1	16	I_DC-57:DG57_J	0.076	0.282	0.135	11.776	-7.253	3.647
1	22	I_DC-51:DG51_J	1.922	-0.283	0.091	13.022	-21.864	3.04
1	25	I_DC-48:DG48_J	0.65	0.115	0.423	14.991	-3.536	0.526
1	26	I_DC-47:DG47_J	0.412	0.631	-0.888	42.229	-22.875	8.002
1	43	I_DC-29:DG29_J	-1.615	0.458	0.619	3.192	-7.996	4.867
1	46	I_DC-26:DG26_J	0.759	-0.464	-0.807	9.245	-12.51	0.865
1	48	I_DC-24:DG24_J	0.4	-0.161	0.024	-7.29	-2.032	0.69
1	49	I_DC-23:DG23_J	0.137	0.04	0.057	-2.102	-10.636	-3.138
1	52	I_DC-20:DG20_J	-0.609	-0.088	-0.806	28.831	-18.269	4.257
1	58	I_DC-13:DG13_J	1.686	-0.296	1.273	-6.911	-16.974	-12.881
1	64	I_DC-7:DG7_J	0.893	0.068	-0.463	19.809	-11.427	1.445
1	67	I_DC-4:DG4_J	-0.469	-0.187	0.821	-4.902	-15.767	-0.912
1	73	I_DC2:DG-2_J	1.015	0.059	0.034	-2.352	-9.088	2.669
1	76	I_DC5:DG-5_J	0.901	-0.43	0.0	4.195	-6.277	-1.377
1	81	I_DC10:DG-10_J	0.174	-0.026	-0.516	16.222	-6.283	-1.303
1	85	I_DC14:DG-14_J	0.831	-0.275	-0.092	-0.001	10.568	0.029
1	86	I_DC15:DG-15_J	-1.107	0.288	0.022	5.739	0.863	5.696
1	94	I_DC27:DG-27_J	-0.175	0.51	0.131	8.967	-27.313	14.199
1	100	I_DC33:DG-33_J	0.22	0.035	0.441	-8.469	-1.176	-0.362
1	101	I_DC34:DG-34_J	0.068	-0.604	1.371	1.162	-5.848	-10.352
1	107	I_DC40:DG-40_J	-0.554	0.409	-0.1	0.027	-10.216	0.958
1	109	I_DC42:DG-42_J	0.245	-0.029	0.981	-24.567	-12.253	1.415
1	119	I_DC55:DG-55_J	0.08	-0.201	0.94	-23.31	-1.823	-2.107
1	122	I_DC58:DG-58_J	0.418	-0.069	0.417	-1.976	-1.436	-1.556
1	15	I_DG-58:DC58_J	-0.976	0.181	0.09	-0.278	-2.033	3.157
1	18	I_DG-55:DC55_J	0.017	0.205	0.461	18.981	-9.637	-1.297
1	31	I_DG-42:DC42_J	0.931	0.467	0.085	-5.516	-6.334	4.179
1	33	I_DG-40:DC40_J	-0.953	-0.201	-0.84	-23.776	-7.512	-7.56
1	39	I_DG-33:DC34_J	-0.403	2.374	0.517	-46.779	-27.555	38.457
1	45	I_DG-27:DC27_J	0.128	-0.172	-0.001	-12.8	-22.333	1.843
1	57	I_DG-15:DC15_J	-0.711	0.16	0.48	11.158	6.346	8.35
1	61	I_DG-10:DC10_J	-0.914	-0.383	-0.645	-2.77	-15.372	-1.735
1	66	I_DG-5:DC5_J	-0.148	-0.014	-0.108	-4.209	-20.84	0.295
1	69	I_DG-2:DC2_J	-0.244	0.094	0.492	7.12	-2.871	9.791
1	75	I_DG4:DC-4_J	0.121	-0.17	0.12	5.396	-24.544	-6.38
1	78	I_DG7:DC-7_J	-0.232	-0.069	-0.655	-12.251	-5.199	-1.768
1	84	I_DG13:DC-13_J	-0.478	0.053	0.159	7.532	6.855	1.446
1	90	I_DG23:DC-23_J	0.717	0.494	-0.639	-30.351	18.192	-5.004
1	91	I_DG24:DC-24_J	0.589	-0.113	-0.737	-13.438	22.561	3.299
1	93	I_DG26:DC-26_J	0.09	-0.23	1.022	15.394	-0.275	-0.776
1	96	I_DG29:DC-29_J	0.562	0.75	0.287	-7.506	-13.011	16.646
1	114	I_DG47:DC-47_J	1.283	1.304	0.43	-19.624	-17.597	14.747
1	115	I_DG48:DC-48_J	-0.909	0.881	0.663	-5.446	-8.136	16.544
1	117	I_DG51:DA-52_J	-0.331	1.399	-1.056	-3.217	-20.963	-2.271
1	121	I_DG57:DC-57_J	-0.228	-0.12	-0.403	-23.127	-12.553	-1.293
1	124	I_DG60:DC-60_J	0.514	0.061	0.532	3.497	-7.922	-0.306
1	125	I_DG61:DC-61_J	0.691	-0.069	-0.166	1.698	-14.155	0.347
1	127	I_DG63:DC-63_J	-0.585	-0.208	-0.571	0.879	-3.327	0.721
1	128	I_DG64:DC-64_J	-0.444	-0.013	0.465	18.408	-5.981	7.471
1	134	I_DG70:DC-70_J	-0.536	-0.292	-0.294	0.007	-8.942	-0.445
1	2	I_DT-71:DA71_J	-0.872	-0.074	0.367	-7.051	-6.744	-2.424
1	6	I_DT-67:DA67_J	0.332	-0.027	0.199	10.421	-10.61	3.735
1	8	I_DT-65:DA65_J	1.09	-0.29	-0.397	6.033	-12.436	-8.5
1	14	I_DT-59:DA59_J	0.084	0.247	-0.677	5.17	-23.625	11.5
1	20	I_DT-53:DA53_J	0.711	0.215	-0.854	11.096	-14.907	-24.095
1	23	I_DT-50:DA50_J	0.745	-0.018	-0.046	9.158	-33.026	3.187
1	32	I_DT-41:DA41_J	-0.028	-0.09	-0.383	-7.561	-9.227	0.884
1	34	I_DT-39:DA39_J	0.213	-0.173	-0.129	-1.901	0.808	-4.802
1	36	I_DT-37:DA37_J	0.352	-0.036	0.315	-10.298	0.453	-0.973
1	37	I_DT-36:DA36_J	-0.447	-0.278	0.027	-5.153	-10.044	-5.23
1	38	I_DT-35:DA35_J	0.282	-0.367	1.242	-12.378	-1.239	3.44
1	44	I_DT-28:DA28_J	-0.315	-0.198	0.303	5.044	-10.292	2.384
1	47	I_DT-25:DA25_J	-0.282	-0.066	0.18	0.349	-30.778	1.773
1	51	I_DT-21:DA21_J	-0.421	-0.125	-0.151	21.602	-2.388	0.43
1	60	I_DT-11:DA11_J	1.271	-0.103	0.406	31.821	7.649	-3.512
1	62	I_DT-9:DA9_J	-0.644	-0.09	0.523	-9.067	-20.979	-0.306
1	63	I_DT-8:DA8_J	0.15	-0.085	-0.096	2.259	-12.405	5.384
1	68	I_DT-3:DA3_J	-0.112	0.205	0.028	-6.458	-15.476	-6.146
1	72	I_DT1:DA-1_J	-0.02	-0.097	0.026	-7.868	-13.964	0.919
1	77	I_DT6:DA-6_J	-0.323	-0.114	-0.053	7.662	-33.902	-4.903
1	83	I_DT12:DA-12_J	0.549	-0.272	-0.602	0.792	-19.77	5.739
1	87	I_DT16:DA-16_J	-0.207	0.29	0.256	10.872	10.297	1.696
1	88	I_DT18:DA-18_J	-0.889	0.068	-0.67	10.903	-19.783	7.07
1	89	I_DT19:DA-19_J	-0.307	0.39	-1.12	19.112	9.751	-14.52
1	97	I_DT30:DA-30_J	0.07	0.271	-0.125	-5.213	-18.276	3.2
1	98	I_DT31:DA-31_J	1.017	0.166	0.549	-13.118	1.724	0.592
1	99	I_DT32:DA-32_J	-0.079	0.115	-0.132	-9.791	-17.056	-19.384
1	105	I_DT38:DA-38_J	-1.529	0.16	-0.719	0.437	-8.112	9.689
1	110	I_DT43:DA-43_J	0.12	0.425	0.155	-19.111	-17.105	0.104
1	111	I_DT44:DA-44_J	-0.576	-0.032	1.065	-20.624	-5.819	-6.705
1	112	I_DT45:DA-45_J	-0.419	-0.024	1.299	-20.469	-5.651	0.794
1	113	I_DT46:DA-46_J	-0.24	0.5	1.016	-14.396	-35.332	7.621
1	118	I_DT54:DA-54_J	-0.161	-0.139	-0.434	10.3	-29.356	5.454
1	120	I_DT56:DA-56_J	-0.203	-0.292	0.744	-15.836	-14.001	0.973
1	126	I_DT62:DA-62_J	0.412	-0.374	-0.959	9.144	-15.633	6.292
1	130	I_DT66:DA-66_J	0.371	0.033	0.034	11.717	-9.454	-1.978
1	132	I_DT68:DA-68_J	-0.158	-0.155	-0.057	3.111	-13.309	2.396
1	133	I_DT69:DA-69_J	0.047	-0.209	0.066	-3.268	-8.794	-2.625
1	136	I_DT72:DA-72_J	-0.015	-0.397	-0.752	18.874	-4.249	-1.24

The above values were obtained using first alternate conformation only and calculated by 3DNA program.
Xiang-Jun Lu & Wilma K. Olson (2003). '3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures', Nucleic Acids Res.31(17), 5108-21.
Xiang-Jun Lu & Wilma K. Olson (2008). '3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures', Nat Protoc.3(7), 1213-27.