A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 22-Jun-2022 number of released structures: 12128
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NDB ID: 5DNM  PDB ID: 5DNM 


Base Pair Morphology Step Parameters

CSV Format

Model NumberStep NumberStep NameShiftSlideRiseTiltRollTwistX-DisplacementY-DisplacementHelical RiseInclinationTipHelical Twist
11II_DA-72DT-71:DA71DT72_JJ-0.744-1.3843.289-1.756.93235.338-3.1930.9613.00511.2762.84736.031
14II_DA-69DA-68:DT68DT69_JJ-0.9020.4873.089-5.32-2.01539.9940.9230.7333.152-2.9287.73140.38
15II_DA-68DT-67:DA67DT68_JJ0.594-0.6193.403-0.0190.62130.885-1.286-1.1183.391.1670.03530.891
17II_DA-66DT-65:DA65DT66_JJ-0.321-1.0613.4214.31-3.97234.984-1.1251.1963.455-6.551-7.10835.456
111II_DA-62DC-61:DG61DT62_JJ0.824-0.6553.0858.9994.11229.086-2.0210.1583.0787.904-17.29930.689
117II_DA-56DG-55:DC55DT56_JJ0.519-0.1053.3881.1861.19728.025-0.509-0.7793.42.47-2.44528.075
119II_DA-54DT-53:DA53DT54_JJ-0.843-0.793.0070.933-2.01735.582-1.0211.5023.024-3.297-1.52535.649
121II_DA-52DC-51:DG51DT52_JJ0.070.0182.431-3.4383.52632.403-0.419-0.5642.46.2736.11632.765
124II_DA-49DC-48:DG48DT49_JJ0.581-0.6632.9091.2355.80831.369-2.13-0.862.76510.623-2.25831.912
127II_DA-46DA-45:DT45DT46_JJ0.6780.3653.6724.303-7.28138.7751.495-0.4343.6-10.811-6.38939.652
128II_DA-45DA-44:DT44DT45_JJ1.142-0.5543.32-1.688-6.62532.8490.153-2.2633.305-11.5582.94533.533
129II_DA-44DA-43:DT43DT44_JJ-0.03-0.4223.1916.6080.535.758-0.7450.9473.130.806-10.64936.347
130II_DA-43DG-42:DC42DT43_JJ0.393-0.8993.6580.942-1.43441.454-1.098-0.4433.694-2.024-1.3341.488
135II_DA-38DT-37:DA37DT38_JJ0.697-0.6613.121-0.691-6.96238.841-0.181-1.1123.176-10.3671.02939.443
140II_DA-32DA-31:DT31DT32_JJ0.1280.122.818-8.8728.64534.251-0.849-1.2732.65714.1214.4936.359
141II_DA-31DA-30:DT30DT31_JJ0.1990.0013.251-6.1868.44433.337-1.266-1.263.07514.28710.46734.897
142II_DA-30DC-29:DG29DT30_JJ-0.012-0.8593.341-0.0354.54126.064-3.0820.0183.1499.9720.07626.45
150II_DA-22DT-21:DA21DT22_JJ0.366-0.913.3333.866-4.01825.081-0.8580.3193.45-9.109-8.76425.683
153II_DA-19DA-18:DT18DT19_JJ0.3860.3543.3380.6265.70742.042-0.108-0.4683.3617.91-0.86842.414
154II_DA-18DA-17:DT17DT18_JJ-0.65-0.1233.234-4.113-2.8739.9240.1460.4793.283-4.1835.99540.225
155II_DA-17DA-16:DT16DT17_JJ-0.269-0.6922.923-3.272-8.62734.8630.0120.0063.016-14.0965.34736.027
156II_DA-16DG-15:DC15DT16_JJ0.985-0.2453.091-0.7252.28329.638-0.927-2.0623.0394.4541.41429.733
158II_DA-12DT-11:DA11DT12_JJ0.941-0.2582.88-3.274-2.7734.858-0.067-1.9852.795-4.6035.43935.113
164II_DA-6DG-5:DC5DT6_JJ0.7390.4423.217-2.36.94125.62-0.845-2.2023.14815.2625.05626.626
169II_DA-1DA0:DT0DT1_JJ-0.595-0.1273.349-4.6478.15335.514-1.3530.2883.2913.0877.45936.694
170II_DA0DT1:DA-1DT0_JJ-0.066-0.9163.3170.9518.81226.773-3.8820.3522.87218.4-1.98728.177
173II_DA3DG4:DC-4DT-3_JJ0.1040.6853.4740.942-2.76838.9081.379-0.0363.421-4.149-1.41239.013
178II_DA8DA9:DT-9DT-8_JJ-0.16-0.033.2810.2811.17330.38-0.2940.3613.2762.238-0.53630.403
179II_DA9DC10:DG-10DT-9_JJ0.305-0.1592.9744.931.90929.758-0.660.332.9693.681-9.50630.214
181II_DA11DT12:DA-12DT-11_JJ0.283-0.2453.1983.1068.7330.158-2.0340.0423.02516.301-5.831.518
190II_DA25DG26:DC-26DT-25_JJ1.98-0.0572.8813.098-12.75430.7251.841-2.9792.861-22.808-5.5433.349
193II_DA28DG29:DC-29DT-28_JJ-0.0160.8142.945-12.2912.58541.250.877-1.0842.883.5716.97843.04
1100II_DA35DA36:DT-36DT-35_JJ0.291-0.7642.853-2.029-1.03933.194-1.183-0.8042.853-1.8173.54633.27
1101II_DA36DA37:DT-37DT-36_JJ-0.019-0.2443.221-0.409-7.00239.690.43-0.0183.217-10.2160.59640.28
1102II_DA37DT38:DA-38DT-37_JJ0.596-1.4833.7357.157-5.40226.348-1.5150.8413.976-11.438-15.15327.806
1104II_DA39DC40:DG-40DT-39_JJ0.679-0.5223.014-4.4021.77831.793-1.231-1.9392.8633.2237.97932.136
1106II_DA41DC42:DG-42DT-41_JJ0.747-0.7593.6-9.915-1.79537.521-0.905-2.4313.336-2.73115.08538.803
1114II_DA50DG51:DA-52DC-51_JJ0.256-0.113.678-0.565.20242.102-0.746-0.4183.6367.2080.77642.412
1121II_DA59DG60:DC-60DT-59_JJ-0.257-0.1943.919-0.569.66428.996-2.6560.3563.6718.6571.08130.537
1127II_DA65DT66:DA-66DT-65_JJ0.114-0.8533.026-0.566-0.36538.503-1.251-0.2383.032-0.5530.85938.509
1129II_DA67DT68:DA-68DT-67_JJ-0.369-0.5323.2031.671-1.97131.141-0.6220.9963.206-3.662-3.10631.246
1133II_DA71DT72:DA-72DT-71_JJ0.844-1.1743.0943.4269.57626.945-4.301-1.0052.61619.684-7.04328.767
13II_DC-70DA-69:DT69DG70_JJ-0.0080.4283.1961.9076.62631.203-0.4130.3573.21112.133-3.49231.937
19II_DC-64DC-63:DG63DG64_JJ0.243-0.4443.3793.8562.4926.935-1.5790.4763.3265.296-8.20427.316
110II_DC-63DA-62:DT62DG63_JJ-0.581-0.2123.324-10.7028.76737.099-1.383-0.4463.23513.22816.14939.51
112II_DC-61DC-60:DG60DG61_JJ0.147-0.0083.5893.7969.31938.224-1.2210.2753.49113.939-5.67839.479
113II_DC-60DT-59:DA59DG60_JJ-0.2351.0353.0775.5538.60627.6970.2311.6243.14617.247-11.1329.495
116II_DC-57DA-56:DT56DG57_JJ0.3552.4753.282-2.566-18.55651.03.728-0.5292.299-20.7662.87154.114
122II_DC-51DT-50:DA50DG51_JJ-0.2840.5453.0435.8397.64830.654-0.311.5032.98614.038-10.71832.094
125II_DC-48DC-47:DG47DG48_JJ0.1610.4052.56215.5022.32629.5680.3941.7872.3774.205-28.03133.384
126II_DC-47DA-46:DT46DG47_JJ-0.032.2473.514-4.352-6.71940.6773.91-0.4333.107-9.5546.18941.425
143II_DC-29DT-28:DA28DG29_JJ0.675-0.1013.3758.0086.51139.084-0.917-0.033.3859.531-11.72340.372
146II_DC-26DT-25:DA25DG26_JJ-0.510.7653.641-2.594-3.06530.8912.0730.4013.58-5.7254.84431.144
148II_DC-24DC-23:DG23DG24_JJ-0.6050.3443.105-3.976-0.28437.9720.5610.4453.147-0.4356.0938.173
149II_DC-23DA-22:DT22DG23_JJ-0.0390.6572.938-6.399-0.57941.0680.981-0.5552.902-0.8199.05541.546
152II_DC-20DA-19:DT19DG20_JJ-0.8260.6664.072-5.08815.28336.45-1.3460.4414.09623.0987.6939.739
157II_DC-13DA-12:DT12DG13_JJ-0.1721.5843.1242.704-19.38431.7384.6270.5681.864-31.934-4.45437.155
163II_DC-7DA-6:DT6DG7_JJ-0.882.0683.9883.9020.83244.1792.6461.6053.9361.103-5.17544.35
166II_DC-4DT-3:DA3DG4_JJ-0.4390.33.387.0862.54236.6590.1261.643.2553.99-11.12237.398
172II_DC2DA3:DT-3DG-2_JJ-1.0160.9313.185-0.912.44625.8961.4022.0093.295.442.02326.025
175II_DC5DT6:DA-6DG-5_JJ-0.9780.963.2781.845-8.91831.1933.2132.0582.842-16.158-3.34232.464
180II_DC10DA11:DT-11DG-10_JJ0.0590.5423.9020.07515.24937.633-1.315-0.0753.83322.54-0.1140.501
184II_DC14DC15:DG-15DG-14_JJ0.2871.8635.1277.443-56.3840.6274.5820.1341.719-56.842-7.50468.89
185II_DC15DT16:DA-16DG-15_JJ0.52-0.1423.393-0.9015.38734.176-1.097-1.0173.3189.0951.52134.597
192II_DC27DA28:DT-28DG-27_JJ0.5071.1144.0080.77112.56335.886-0.352-0.6534.16319.66-1.20637.961
198II_DC33DC34:DG-34DG-33_JJ-0.9240.7133.552-8.101-3.94630.0842.1420.0173.555-7.39615.18431.374
199II_DC34DA35:DT-35DG-34_JJ0.1590.8463.6247.606-18.49139.582.9740.5492.951-25.435-10.46344.162
1105II_DC40DA41:DT-41DG-40_JJ-0.1310.0123.4622.58416.33135.298-2.0970.5323.15225.291-4.00238.867
1107II_DC42DT43:DA-43DG-42_JJ-0.391-0.4713.0378.775-0.86236.13-0.6331.6882.878-1.366-13.89437.155
1117II_DC55DT56:DA-56DG-55_JJ-0.887-0.2653.0153.291-2.07131.022-0.1352.2132.919-3.854-6.12331.259
1120II_DC58DA59:DT-59DG-58_JJ0.0452.1922.897-7.179-9.04745.7233.356-0.5422.413-11.439.06947.083
115II_DG-58DC-57:DG57DC58_JJ-0.0690.2962.8681.5288.5228.133-1.0430.4272.82617.023-3.05329.409
118II_DG-55DA-54:DT54DC55_JJ-0.023-0.3273.6924.363-5.78741.7090.220.5383.683-8.054-6.07242.306
131II_DG-42DT-41:DA41DC42_JJ-0.063-0.3613.4485.5053.06729.899-1.3231.2643.3315.864-10.52330.541
133II_DG-40DT-39:DA39DC40_JJ-0.254-0.092.99-7.847-4.67537.1720.407-0.5262.971-7.212.08638.239
139II_DG-33DA-32:DT32DC34_JJ-0.1293.2923.58-24.8847.9448.892.999-1.6243.7068.89827.88855.05
145II_DG-27DC-26:DG26DC27_JJ0.4911.352.6026.282-5.68141.3032.335-0.1782.449-7.953-8.79442.125
160II_DG-10DT-9:DA9DC10_JJ-0.407-0.1823.564-10.6561.91932.853-0.636-1.1443.5073.28418.23534.545
165II_DG-5DC-4:DG4DC5_JJ-0.1260.9533.518-8.508-16.44543.6322.582-0.5622.971-21.03510.88247.221
168II_DG-2DA-1:DT1DC2_JJ-1.1360.2983.5160.9487.43335.021-0.671.9963.47412.181-1.55435.789
174II_DG4DC5:DG-5DC-4_JJ1.160.6313.3264.461-2.57941.491.163-1.1453.384-3.623-6.26841.794
177II_DG7DA8:DT-8DC-7_JJ-0.7030.8413.058-9.7957.73137.7240.347-0.0963.23911.57514.66739.663
183II_DG13DC14:DG-14DC-13_JJ0.275-0.4863.6540.4397.14939.083-1.636-0.3483.51810.578-0.6539.709
188II_DG23DG24:DC-24DC-23_JJ-0.3820.3463.6890.688-16.98941.2842.2020.5763.302-22.959-0.92944.507
189II_DG24DA25:DT-25DC-24_JJ-2.2631.3453.25-10.256-17.70743.7613.0441.972.96-22.36212.95248.095
191II_DG26DC27:DG-27DC-26_JJ0.00.2143.5058.5451.72830.730.0521.6683.3893.181-15.73131.914
194II_DG29DT30:DA-30DC-29_JJ-1.239-0.6513.0782.2099.06428.694-2.9142.7872.65317.708-4.31530.142
1112II_DG47DG48:DC-48DC-47_JJ-0.7070.7662.645-2.7072.49620.1811.2260.982.7887.0487.64420.511
1113II_DG48DA50:DC-51DC-48_JJ0.9721.1837.061-3.92910.69276.8760.283-1.0197.1038.5553.14477.586
1115II_DG51DT54:DA-54DA-52_JJ0.078-2.2036.78214.1761.45371.541-1.9550.8986.6591.231-12.00872.76
1119II_DG57DC58:DG-58DC-57_JJ-0.1340.5852.752-10.3841.7828.4420.813-1.5382.6663.47520.27530.293
1122II_DG60DG61:DC-61DC-60_JJ-0.072-0.6823.3552.3634.8135.323-1.8150.4623.2267.871-3.86635.714
1123II_DG61DT62:DA-62DC-61_JJ-0.178-0.3312.9946.6848.84130.905-1.9521.3482.70415.961-12.06832.787
1125II_DG63DG64:DC-64DC-63_JJ0.3760.1482.948-8.6181.37828.8480.035-2.2862.7282.6916.81930.112
1126II_DG64DA65:DT-65DC-64_JJ-0.937-0.4433.6120.3870.54837.115-0.7761.5293.5960.861-0.60837.121
1132II_DG70DA71:DT-71DC-70_JJ-0.280.0773.189-2.611-3.4743.820.4220.1343.185-4.6363.48844.024
12II_DT-71DC-70:DG70DA71_JJ0.665-0.093.1773.4172.16739.644-0.377-0.593.2113.185-5.02339.842
16II_DT-67DA-66:DT66DA67_JJ-0.109-0.2763.273-1.943-6.3843.0490.248-0.0423.281-8.6332.62843.538
18II_DT-65DC-64:DG64DA65_JJ0.892-0.5113.122-2.915-1.79335.1-0.592-1.8823.062-2.9654.81935.261
114II_DT-59DG-58:DC58DA59_JJ0.0592.2023.507-5.447-0.89240.583.253-0.7183.425-1.2797.80940.938
120II_DT-53DA-52:DT52DA53_JJ0.259-2.1654.0562.99515.429.104-6.6630.0992.62428.209-5.48632.983
123II_DT-50DA-49:DT49DA50_JJ0.098-0.3453.415-8.80110.44227.513-2.762-1.9642.92920.43717.22430.657
132II_DT-41DG-40:DC40DA41_JJ-0.156-0.4173.762-2.30822.15824.378-4.961-0.1642.53842.774.45432.91
134II_DT-39DA-38:DT38DA39_JJ-0.476-1.3393.503-0.24810.031.686-4.0420.7912.95917.7690.44133.189
136II_DT-37DT-36:DA36DA37_JJ-0.289-0.6562.9664.331-2.5636.981-0.7180.9712.951-4.013-6.78937.31
137II_DT-36DT-35:DA35DA36_JJ0.218-0.3263.715-7.3381.333.414-0.785-1.6763.5742.22612.56934.212
138II_DT-35DG-33:DC34DA35_JJ-1.4593.9965.30319.307-0.37565.0773.6162.4784.739-0.341-17.54967.579
144II_DT-28DG-27:DC27DA28_JJ-0.721.0163.7081.6375.12441.7040.8071.1993.7727.161-2.28742.034
147II_DT-25DC-24:DG24DA25_JJ1.3381.4833.6263.403-0.75843.2432.089-1.443.69-1.027-4.60943.377
151II_DT-21DC-20:DG20DA21_JJ1.2680.1813.13213.3097.0132.719-0.749-0.0773.35211.704-22.22135.925
159II_DT-11DG-10:DC10DA11_JJ0.5450.6045.11115.44243.14119.176-5.0621.4192.72464.484-23.08149.472
161II_DT-9DT-8:DA8DA9_JJ0.306-0.0023.05.6620.84535.249-0.1160.2593.0111.384-9.27435.696
162II_DT-8DC-7:DG7DA8_JJ1.1890.8772.8939.6143.13438.8140.944-0.7043.1474.622-14.17540.06
167II_DT-3DG-2:DC2DA3_JJ1.5140.9752.999-2.3781.74634.251.402-2.8992.9362.9584.02934.373
171II_DT1DC2:DG-2DA-1_JJ0.5230.2083.2022.9934.4840.953-0.181-0.4243.2356.37-4.25541.291
176II_DT6DG7:DC-7DA-6_JJ1.2681.5143.8595.3364.38543.111.521-1.0794.1075.922-7.20643.634
182II_DT12DG13:DC-13DA-12_JJ-0.1230.2413.185-8.1255.20232.533-0.41-1.0763.1259.04114.1233.897
186II_DT16DT18:DA-18DA-16_JJ1.2060.1626.3715.139-8.71977.2210.601-0.1266.438-6.903-11.98778.871
187II_DT18DT19:DA-19DA-18_JJ0.4190.2033.3472.11-6.35743.7080.878-0.3553.304-8.479-2.81544.193
195II_DT30DT31:DA-31DA-30_JJ-0.01-0.3563.654-0.7817.27334.433-1.79-0.1133.50812.1171.335.179
196II_DT31DT32:DA-32DA-31_JJ-0.957-0.3743.0765.0656.07332.445-1.5672.4312.78510.672-8.933.37
197II_DT32DC33:DG-33DA-32_JJ1.9380.6273.5040.2564.18340.00.398-2.7873.5616.095-0.37340.21
1103II_DT38DA39:DT-39DA-38_JJ-0.054-0.1094.002-2.24611.14439.205-1.661-0.2263.8316.1993.26540.757
1108II_DT43DT44:DA-44DA-43_JJ-0.311-0.3953.394-8.261-7.0233.4870.461-0.7983.386-11.80513.89335.15
1109II_DT44DT45:DA-45DA-44_JJ0.082-0.2583.2811.641-5.87140.2350.2860.0663.286-8.476-2.36940.675
1110II_DT45DT46:DA-46DA-45_JJ-0.4240.8553.1336.069-14.10938.7172.5671.1842.589-20.334-8.74741.543
1111II_DT46DG47:DC-47DA-46_JJ0.4161.8483.0282.6152.14840.9452.413-0.3243.1363.065-3.73141.078
1116II_DT54DC55:DG-55DA-54_JJ0.035-0.5674.167-10.2282.25838.533-1.162-1.5513.9923.34715.16139.879
1118II_DT56DG57:DC-57DA-56_JJ-0.8662.9593.3410.325-11.23451.394.0290.9982.679-12.78-0.3752.523
1124II_DT62DG63:DC-63DA-62_JJ-0.3090.0483.748-2.51318.37126.594-3.6990.0373.14735.0384.79332.324
1128II_DT66DA67:DT-67DA-66_JJ-0.052-0.2333.658-3.794-6.96138.6240.583-0.4293.633-10.3915.66339.399
1130II_DT68DT69:DA-69DA-68_JJ0.4510.363.4041.827-0.35539.0630.582-0.4443.417-0.53-2.73139.106
1131II_DT69DG70:DC-70DA-69_JJ0.209-0.0163.263.2757.44227.14-1.7570.3323.14815.425-6.78728.31

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.