PDB Chemical Component DUR
The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.
Bond Distances for DUR
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.392 |
1.344 |
| N1 |
C6 |
1.324 |
1.368 |
| N1 |
C1' |
1.476 |
1.464 |
| C2 |
N3 |
1.371 |
1.347 |
| C2 |
O2 |
1.224 |
1.216 |
| N3 |
C4 |
1.392 |
1.348 |
| N3 |
HN3 |
1.021 |
0.969 |
| C4 |
C5 |
1.455 |
1.415 |
| C4 |
O4 |
1.234 |
1.218 |
| C5 |
C6 |
1.396 |
1.350 |
| C5 |
H5 |
1.102 |
1.080 |
| C6 |
H6 |
1.102 |
1.080 |
| C1' |
C2' |
1.521 |
1.541 |
| C1' |
O4' |
1.471 |
1.437 |
| C1' |
H1' |
1.116 |
1.090 |
| C2' |
C3' |
1.512 |
1.550 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.114 |
1.088 |
| C3' |
C4' |
1.534 |
1.548 |
| C3' |
O3' |
1.431 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| C4' |
O4' |
1.477 |
1.444 |
| C4' |
C5' |
1.542 |
1.530 |
| C4' |
H4' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C5' |
O5' |
1.433 |
1.428 |
| C5' |
H5'1 |
1.114 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.091 |
| O5' |
HO5' |
0.949 |
0.966 |
Bond Angles for DUR
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
123.8 |
120.6 |
| C2 |
N1 |
C1' |
119.1 |
119.7 |
| N1 |
C2 |
N3 |
115.7 |
121.0 |
| N1 |
C2 |
O2 |
124.6 |
119.5 |
| C6 |
N1 |
C1' |
117.1 |
119.7 |
| N1 |
C6 |
C5 |
120.3 |
119.7 |
| N1 |
C6 |
H6 |
117.2 |
120.2 |
| N1 |
C1' |
C2' |
113.3 |
110.0 |
| N1 |
C1' |
O4' |
119.7 |
109.9 |
| N1 |
C1' |
H1' |
97.1 |
109.9 |
| N3 |
C2 |
O2 |
119.7 |
119.5 |
| C2 |
N3 |
C4 |
126.0 |
120.2 |
| C2 |
N3 |
HN3 |
116.2 |
119.8 |
| C4 |
N3 |
HN3 |
117.8 |
119.9 |
| N3 |
C4 |
C5 |
114.2 |
119.4 |
| N3 |
C4 |
O4 |
121.0 |
120.3 |
| C5 |
C4 |
O4 |
124.7 |
120.3 |
| C4 |
C5 |
C6 |
120.1 |
119.1 |
| C4 |
C5 |
H5 |
122.0 |
120.4 |
| C6 |
C5 |
H5 |
117.9 |
120.5 |
| C5 |
C6 |
H6 |
122.5 |
120.1 |
| C2' |
C1' |
O4' |
103.4 |
107.3 |
| C2' |
C1' |
H1' |
115.4 |
109.9 |
| C1' |
C2' |
C3' |
102.8 |
104.2 |
| C1' |
C2' |
H2'1 |
114.7 |
110.4 |
| C1' |
C2' |
H2'2 |
114.7 |
110.5 |
| O4' |
C1' |
H1' |
108.3 |
109.8 |
| C1' |
O4' |
C4' |
107.7 |
107.0 |
| C3' |
C2' |
H2'1 |
114.8 |
110.3 |
| C3' |
C2' |
H2'2 |
114.8 |
110.6 |
| C2' |
C3' |
C4' |
97.6 |
102.1 |
| C2' |
C3' |
O3' |
108.4 |
110.9 |
| C2' |
C3' |
H3' |
117.5 |
110.9 |
| H2'1 |
C2' |
H2'2 |
95.8 |
110.6 |
| C4' |
C3' |
O3' |
109.9 |
111.2 |
| C4' |
C3' |
H3' |
116.2 |
110.8 |
| C3' |
C4' |
O4' |
105.1 |
103.6 |
| C3' |
C4' |
C5' |
110.2 |
110.7 |
| C3' |
C4' |
H4' |
112.2 |
110.6 |
| O3' |
C3' |
H3' |
106.7 |
110.8 |
| C3' |
O3' |
HO3' |
108.5 |
106.8 |
| O4' |
C4' |
C5' |
110.5 |
110.6 |
| O4' |
C4' |
H4' |
111.8 |
110.6 |
| C5' |
C4' |
H4' |
107.1 |
110.5 |
| C4' |
C5' |
O5' |
112.7 |
109.5 |
| C4' |
C5' |
H5'1 |
111.0 |
109.4 |
| C4' |
C5' |
H5'2 |
111.0 |
109.4 |
| O5' |
C5' |
H5'1 |
111.0 |
109.5 |
| O5' |
C5' |
H5'2 |
111.0 |
109.5 |
| C5' |
O5' |
HO5' |
112.8 |
106.9 |
| H5'1 |
C5' |
H5'2 |
99.4 |
109.5 |
Torsion Angles for DUR
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
177.3 |
179.7 |
| C2 |
N1 |
C6 |
C5 |
358.8 |
0.3 |
| C2 |
N1 |
C6 |
H6 |
178.8 |
180.2 |
| C2 |
N1 |
C1' |
C2' |
92.8 |
300.4 |
| C2 |
N1 |
C1' |
O4' |
215.2 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
331.1 |
179.3 |
| N3 |
C2 |
N1 |
O2 |
177.6 |
179.5 |
| N1 |
C2 |
N3 |
C4 |
359.3 |
0.6 |
| N1 |
C2 |
N3 |
HN3 |
179.4 |
180.2 |
| C2 |
N1 |
C6 |
C1' |
182.7 |
180.3 |
| C6 |
N1 |
C2 |
N3 |
1.3 |
359.5 |
| C6 |
N1 |
C2 |
O2 |
183.7 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
275.3 |
120.7 |
| C6 |
N1 |
C1' |
O4' |
37.8 |
238.5 |
| C6 |
N1 |
C1' |
H1' |
153.6 |
359.6 |
| C4 |
C5 |
C6 |
N1 |
0.4 |
360.0 |
| N1 |
C6 |
C5 |
H5 |
180.4 |
179.9 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| C2 |
N1 |
C1' |
C6 |
177.5 |
179.7 |
| C1' |
N1 |
C2 |
N3 |
184.0 |
179.7 |
| C1' |
N1 |
C2 |
O2 |
6.4 |
0.3 |
| C1' |
N1 |
C6 |
C5 |
176.1 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
356.1 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
237.5 |
242.1 |
| C2' |
C1' |
N1 |
H1' |
121.7 |
121.1 |
| N1 |
C1' |
C2' |
C3' |
169.0 |
121.7 |
| N1 |
C1' |
C2' |
H2'1 |
294.3 |
240.1 |
| N1 |
C1' |
C2' |
H2'2 |
43.7 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
244.2 |
239.0 |
| N1 |
C1' |
O4' |
C4' |
221.1 |
214.0 |
| N3 |
C2 |
N1 |
C6 |
1.3 |
359.5 |
| N3 |
C2 |
N1 |
C1' |
184.0 |
179.7 |
| N1 |
C2 |
N3 |
O2 |
182.3 |
180.5 |
| C4 |
N3 |
C2 |
HN3 |
179.9 |
180.3 |
| C2 |
N3 |
C4 |
C5 |
360.0 |
359.7 |
| C2 |
N3 |
C4 |
O4 |
175.8 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
183.7 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
6.4 |
0.3 |
| N1 |
C2 |
O2 |
N3 |
177.5 |
179.5 |
| O2 |
C2 |
N3 |
C4 |
177.1 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
357.1 |
359.7 |
| C4 |
N3 |
C2 |
O2 |
177.1 |
180.0 |
| C2 |
N3 |
C4 |
HN3 |
180.1 |
179.7 |
| C5 |
C4 |
N3 |
O4 |
184.2 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.2 |
0.0 |
| N3 |
C4 |
C5 |
H5 |
180.2 |
180.1 |
| HN3 |
N3 |
C2 |
O2 |
357.1 |
359.7 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.3 |
| HN3 |
N3 |
C4 |
C5 |
179.9 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
355.7 |
0.0 |
| N1 |
C6 |
C5 |
C4 |
0.4 |
360.0 |
| C5 |
C4 |
N3 |
HN3 |
179.9 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
175.6 |
180.0 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
H6 |
180.4 |
180.1 |
| O4 |
C4 |
N3 |
HN3 |
355.7 |
0.0 |
| N3 |
C4 |
O4 |
C5 |
184.7 |
180.0 |
| O4 |
C4 |
C5 |
C6 |
184.6 |
180.0 |
| O4 |
C4 |
C5 |
H5 |
4.6 |
0.1 |
| C5 |
C6 |
N1 |
C1' |
176.1 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C6 |
C5 |
C4 |
O4 |
184.6 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| H5 |
C5 |
C4 |
O4 |
4.6 |
0.1 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.9 |
| H5 |
C5 |
C6 |
H6 |
0.4 |
0.0 |
| H6 |
C6 |
N1 |
C1' |
356.1 |
359.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
H5 |
0.4 |
0.0 |
| N1 |
C1' |
C2' |
O4' |
131.1 |
119.5 |
| N1 |
C1' |
C2' |
H1' |
249.2 |
238.9 |
| O4' |
C1' |
C2' |
H1' |
118.1 |
119.4 |
| C2' |
C1' |
O4' |
C4' |
348.3 |
333.5 |
| C3' |
C2' |
C1' |
H2'1 |
234.8 |
241.5 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
118.9 |
| C1' |
C2' |
C3' |
C4' |
312.7 |
20.7 |
| C1' |
C2' |
C3' |
O3' |
66.8 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
187.8 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.5 |
237.3 |
| N1 |
C1' |
O4' |
C2' |
232.8 |
240.5 |
| N1 |
C1' |
O4' |
H1' |
109.8 |
121.1 |
| C2' |
C1' |
O4' |
H1' |
237.1 |
240.6 |
| O4' |
C1' |
C2' |
C3' |
37.9 |
2.2 |
| O4' |
C1' |
C2' |
H2'1 |
163.1 |
120.6 |
| O4' |
C1' |
C2' |
H2'2 |
272.6 |
243.3 |
| C3' |
C4' |
O4' |
C1' |
341.7 |
40.0 |
| C1' |
O4' |
C4' |
C5' |
100.5 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
219.7 |
281.4 |
| N1 |
C1' |
H1' |
C2' |
120.1 |
121.2 |
| N1 |
C1' |
H1' |
O4' |
235.4 |
239.0 |
| C2' |
C1' |
H1' |
O4' |
115.3 |
117.8 |
| H1' |
C1' |
C2' |
C3' |
279.8 |
242.8 |
| H1' |
C1' |
C2' |
H2'1 |
45.0 |
1.3 |
| H1' |
C1' |
C2' |
H2'2 |
154.5 |
123.9 |
| H1' |
C1' |
O4' |
C4' |
111.2 |
92.9 |
| C3' |
C2' |
C1' |
O4' |
37.9 |
2.2 |
| C3' |
C2' |
C1' |
H1' |
279.8 |
242.8 |
| C1' |
C2' |
C3' |
H2'1 |
125.2 |
118.6 |
| C1' |
C2' |
C3' |
H2'2 |
234.8 |
241.3 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.6 |
122.7 |
| C4' |
C3' |
C2' |
O3' |
246.0 |
241.5 |
| C4' |
C3' |
C2' |
H3' |
124.9 |
118.0 |
| C2' |
C3' |
C4' |
O4' |
40.3 |
323.2 |
| C2' |
C3' |
C4' |
C5' |
281.2 |
204.6 |
| C2' |
C3' |
C4' |
H4' |
162.1 |
81.8 |
| O3' |
C3' |
C2' |
H3' |
238.9 |
236.4 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
61.5 |
| H2'1 |
C2' |
C1' |
O4' |
163.1 |
120.6 |
| H2'1 |
C2' |
C1' |
H1' |
45.0 |
1.3 |
| C1' |
C2' |
H2'1 |
C3' |
241.3 |
245.3 |
| C1' |
C2' |
H2'1 |
H2'2 |
120.6 |
122.6 |
| C3' |
C2' |
H2'1 |
H2'2 |
239.3 |
237.3 |
| H2'1 |
C2' |
C3' |
C4' |
187.5 |
262.1 |
| H2'1 |
C2' |
C3' |
O3' |
301.6 |
20.6 |
| H2'1 |
C2' |
C3' |
H3' |
62.6 |
144.1 |
| H2'2 |
C2' |
C1' |
O4' |
272.6 |
243.3 |
| H2'2 |
C2' |
C1' |
H1' |
154.5 |
123.9 |
| C1' |
C2' |
H2'2 |
C3' |
118.7 |
114.9 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.4 |
237.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
120.7 |
122.5 |
| H2'2 |
C2' |
C3' |
C4' |
78.0 |
139.4 |
| H2'2 |
C2' |
C3' |
O3' |
192.0 |
257.8 |
| H2'2 |
C2' |
C3' |
H3' |
313.1 |
21.4 |
| C1' |
O4' |
C4' |
C3' |
341.7 |
40.0 |
| C4' |
C3' |
C2' |
H2'1 |
187.5 |
262.1 |
| C4' |
C3' |
C2' |
H2'2 |
78.0 |
139.4 |
| C2' |
C3' |
C4' |
O3' |
112.8 |
118.3 |
| C2' |
C3' |
C4' |
H3' |
234.1 |
241.9 |
| O3' |
C3' |
C4' |
H3' |
121.3 |
123.7 |
| C4' |
C3' |
O3' |
HO3' |
285.7 |
174.3 |
| O4' |
C4' |
C3' |
C5' |
119.1 |
118.6 |
| O4' |
C4' |
C3' |
H4' |
238.2 |
241.4 |
| C5' |
C4' |
C3' |
H4' |
119.2 |
122.8 |
| C3' |
C4' |
C5' |
O5' |
180.9 |
177.8 |
| C3' |
C4' |
C5' |
H5'1 |
306.1 |
57.8 |
| C3' |
C4' |
C5' |
H5'2 |
55.6 |
297.8 |
| O3' |
C3' |
C2' |
H2'1 |
301.6 |
20.6 |
| O3' |
C3' |
C2' |
H2'2 |
192.0 |
257.8 |
| C2' |
C3' |
O3' |
C4' |
254.3 |
247.2 |
| C2' |
C3' |
O3' |
H3' |
127.5 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
233.2 |
236.4 |
| O3' |
C3' |
C4' |
O4' |
287.4 |
205.0 |
| O3' |
C3' |
C4' |
C5' |
168.4 |
86.3 |
| O3' |
C3' |
C4' |
H4' |
49.2 |
323.5 |
| H3' |
C3' |
C2' |
H2'1 |
62.6 |
144.1 |
| H3' |
C3' |
C2' |
H2'2 |
313.1 |
21.4 |
| C2' |
C3' |
H3' |
C4' |
115.1 |
112.6 |
| C2' |
C3' |
H3' |
O3' |
238.1 |
236.4 |
| C4' |
C3' |
H3' |
O3' |
123.0 |
123.9 |
| H3' |
C3' |
C4' |
O4' |
166.1 |
81.3 |
| H3' |
C3' |
C4' |
C5' |
47.1 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
287.9 |
199.8 |
| H3' |
C3' |
O3' |
HO3' |
52.5 |
297.9 |
| C4' |
O4' |
C1' |
H1' |
111.2 |
92.9 |
| O4' |
C4' |
C3' |
O3' |
287.4 |
205.0 |
| O4' |
C4' |
C3' |
H3' |
166.1 |
81.3 |
| C3' |
C4' |
O4' |
C5' |
241.2 |
241.4 |
| C3' |
C4' |
O4' |
H4' |
122.0 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
240.8 |
237.2 |
| O4' |
C4' |
C5' |
O5' |
65.1 |
63.6 |
| O4' |
C4' |
C5' |
H5'1 |
190.4 |
303.5 |
| O4' |
C4' |
C5' |
H5'2 |
299.9 |
183.6 |
| C5' |
C4' |
C3' |
O3' |
168.4 |
86.3 |
| C5' |
C4' |
C3' |
H3' |
47.1 |
322.7 |
| C3' |
C4' |
C5' |
O4' |
115.7 |
114.3 |
| C3' |
C4' |
C5' |
H4' |
237.7 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
122.0 |
122.8 |
| O5' |
C5' |
C4' |
H5'1 |
234.8 |
120.1 |
| O5' |
C5' |
C4' |
H5'2 |
125.2 |
240.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
120.0 |
| H4' |
C4' |
C3' |
O3' |
49.2 |
323.5 |
| H4' |
C4' |
C3' |
H3' |
287.9 |
199.8 |
| C3' |
C4' |
H4' |
O4' |
242.1 |
245.8 |
| C3' |
C4' |
H4' |
C5' |
121.0 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
238.8 |
237.2 |
| H4' |
C4' |
C5' |
O5' |
303.1 |
300.7 |
| H4' |
C4' |
C5' |
H5'1 |
68.4 |
180.7 |
| H4' |
C4' |
C5' |
H5'2 |
177.9 |
60.7 |
| HO3' |
O3' |
C3' |
H3' |
52.5 |
297.9 |
| O5' |
C5' |
C4' |
H4' |
303.1 |
300.7 |
| C4' |
C5' |
O5' |
H5'1 |
125.2 |
240.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.8 |
120.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.6 |
240.0 |
| H5'1 |
C5' |
C4' |
H4' |
68.4 |
180.7 |
| C4' |
C5' |
H5'1 |
O5' |
233.8 |
120.1 |
| C4' |
C5' |
H5'1 |
H5'2 |
116.8 |
240.1 |
| O5' |
C5' |
H5'1 |
H5'2 |
243.1 |
120.0 |
| H5'1 |
C5' |
O5' |
HO5' |
54.8 |
300.0 |
| H5'2 |
C5' |
C4' |
H4' |
177.9 |
60.7 |
| C4' |
C5' |
H5'2 |
O5' |
126.2 |
240.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
243.1 |
119.9 |
| O5' |
C5' |
H5'2 |
H5'1 |
116.9 |
240.0 |
| H5'2 |
C5' |
O5' |
HO5' |
305.2 |
60.0 |
| HO5' |
O5' |
C5' |
H5'1 |
54.8 |
300.0 |
| HO5' |
O5' |
C5' |
H5'2 |
305.2 |
60.0 |