PDB Chemical Component DUZ
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 DUZ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
P |
1.610 |
1.610 |
| OP1 |
P |
1.514 |
1.480 |
| P |
OP2 |
1.504 |
1.610 |
| P |
OP3 |
1.595 |
1.610 |
| C2 |
N1 |
1.426 |
1.342 |
| C1' |
N1 |
1.464 |
1.466 |
| N1 |
C6 |
1.336 |
1.358 |
| O2 |
C2 |
1.248 |
1.215 |
| C2 |
N3 |
1.341 |
1.344 |
| N3 |
C4 |
1.338 |
1.350 |
| N3 |
HN3 |
1.001 |
0.970 |
| C4 |
O4 |
1.249 |
1.217 |
| C4 |
C5 |
1.489 |
1.471 |
| C6 |
C5 |
1.385 |
1.381 |
| C5 |
C21 |
1.494 |
1.471 |
| C6 |
H6 |
1.080 |
1.080 |
| C1' |
C2' |
1.520 |
1.541 |
| C1' |
O4' |
1.434 |
1.437 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.516 |
1.549 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.089 |
| C21 |
N23 |
1.334 |
1.348 |
| C21 |
O22 |
1.221 |
1.217 |
| N23 |
C24 |
1.460 |
1.465 |
| N23 |
HN23 |
1.000 |
0.970 |
| C24 |
C25 |
1.521 |
1.507 |
| C24 |
H24 |
1.100 |
1.090 |
| C24 |
H24A |
1.101 |
1.090 |
| C30 |
C25 |
1.403 |
1.382 |
| C25 |
C26 |
1.391 |
1.382 |
| C26 |
C27 |
1.397 |
1.382 |
| C26 |
H26 |
1.080 |
1.081 |
| C28 |
C27 |
1.393 |
1.382 |
| C27 |
H27 |
1.080 |
1.080 |
| C29 |
C28 |
1.391 |
1.382 |
| C28 |
H28 |
1.080 |
1.080 |
| C30 |
C29 |
1.399 |
1.382 |
| C29 |
H29 |
1.080 |
1.081 |
| O3' |
C3' |
1.428 |
1.429 |
| C3' |
C4' |
1.517 |
1.550 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C30 |
H30 |
1.080 |
1.080 |
| O4' |
C4' |
1.426 |
1.444 |
| C4' |
C5' |
1.522 |
1.529 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.426 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| OP2 |
HOP2 |
0.950 |
0.966 |
| OP3 |
HOP3 |
0.950 |
0.968 |
Bond Angles for DUZ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP2 |
110.1 |
109.5 |
| O5' |
P |
OP3 |
100.9 |
109.5 |
| OP1 |
P |
OP2 |
121.7 |
109.5 |
| OP1 |
P |
OP3 |
105.2 |
109.5 |
| OP2 |
P |
OP3 |
109.9 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| C2 |
N1 |
C6 |
120.5 |
121.5 |
| N1 |
C6 |
C5 |
119.4 |
119.3 |
| N1 |
C6 |
H6 |
120.3 |
120.3 |
| O2 |
C2 |
N3 |
118.1 |
118.9 |
| C2 |
N3 |
C4 |
120.5 |
120.4 |
| C2 |
N3 |
HN3 |
119.8 |
119.8 |
| C4 |
N3 |
HN3 |
119.7 |
119.7 |
| N3 |
C4 |
O4 |
119.8 |
120.8 |
| N3 |
C4 |
C5 |
118.9 |
118.5 |
| O4 |
C4 |
C5 |
121.3 |
120.7 |
| C4 |
C5 |
C21 |
123.5 |
121.0 |
| C6 |
C5 |
C21 |
117.4 |
120.9 |
| C5 |
C21 |
N23 |
120.5 |
120.0 |
| C5 |
C21 |
O22 |
117.1 |
120.0 |
| C2' |
C1' |
O4' |
106.0 |
107.3 |
| C2' |
C1' |
H1' |
108.4 |
109.9 |
| C1' |
C2' |
C3' |
102.1 |
104.2 |
| C1' |
C2' |
H2' |
111.3 |
110.5 |
| C1' |
C2' |
H2'A |
111.3 |
110.5 |
| O4' |
C1' |
H1' |
109.5 |
110.0 |
| C1' |
O4' |
C4' |
111.3 |
107.0 |
| C3' |
C2' |
H2' |
111.3 |
110.5 |
| C3' |
C2' |
H2'A |
111.3 |
110.5 |
| C2' |
C3' |
C4' |
105.3 |
102.1 |
| C2' |
C3' |
H3' |
111.9 |
110.9 |
| H2' |
C2' |
H2'A |
109.4 |
110.5 |
| O22 |
C21 |
N23 |
122.4 |
120.0 |
| C21 |
N23 |
C24 |
126.5 |
120.0 |
| C21 |
N23 |
HN23 |
116.7 |
120.0 |
| C24 |
N23 |
HN23 |
116.7 |
120.0 |
| N23 |
C24 |
C25 |
105.7 |
109.5 |
| N23 |
C24 |
H24 |
110.4 |
109.5 |
| N23 |
C24 |
H24A |
110.4 |
109.4 |
| C25 |
C24 |
H24 |
110.4 |
109.5 |
| C25 |
C24 |
H24A |
110.4 |
109.5 |
| C24 |
C25 |
C26 |
120.8 |
120.0 |
| H24 |
C24 |
H24A |
109.5 |
109.5 |
| C25 |
C26 |
C27 |
120.2 |
120.0 |
| C25 |
C26 |
H26 |
119.9 |
120.0 |
| C27 |
C26 |
H26 |
119.9 |
120.0 |
| C26 |
C27 |
H27 |
119.3 |
120.0 |
| C28 |
C27 |
H27 |
119.3 |
120.0 |
| C29 |
C28 |
H28 |
120.7 |
120.0 |
| C30 |
C29 |
H29 |
119.9 |
120.0 |
| O3' |
C3' |
C4' |
103.6 |
110.9 |
| O3' |
C3' |
H3' |
113.4 |
110.9 |
| C4' |
C3' |
H3' |
111.9 |
110.9 |
| C3' |
C4' |
C5' |
114.1 |
110.6 |
| C3' |
C4' |
H4' |
108.7 |
110.7 |
| O4' |
C4' |
C5' |
110.0 |
110.6 |
| O4' |
C4' |
H4' |
109.8 |
110.7 |
| C5' |
C4' |
H4' |
108.5 |
110.5 |
| C4' |
C5' |
O5' |
109.9 |
109.5 |
| C4' |
C5' |
H5' |
109.3 |
109.5 |
| C4' |
C5' |
H5'A |
109.4 |
109.5 |
| O5' |
C5' |
H5' |
109.4 |
109.4 |
| O5' |
C5' |
H5'A |
109.4 |
109.4 |
| H5' |
C5' |
H5'A |
109.5 |
109.5 |
Torsion Angles for DUZ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
O5' |
OP2 |
225.8 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
109.7 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
243.9 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
233.7 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
111.1 |
180.0 |
| O5' |
P |
OP1 |
OP2 |
127.7 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
253.3 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
125.6 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
179.9 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
60.0 |
| O5' |
P |
OP2 |
OP3 |
110.3 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
236.6 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
227.4 |
300.0 |
| O5' |
P |
OP3 |
OP2 |
243.7 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
132.6 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
123.4 |
300.0 |
| C2 |
N1 |
C6 |
C5 |
357.4 |
360.0 |
| C2 |
N1 |
C6 |
H6 |
177.4 |
180.0 |
| C1' |
N1 |
C6 |
H6 |
0.8 |
0.3 |
| N1 |
C6 |
C5 |
C21 |
179.3 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
181.4 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
179.1 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
359.1 |
0.0 |
| N3 |
C2 |
N1 |
C6 |
1.6 |
0.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
O4 |
180.6 |
180.1 |
| C2 |
N3 |
C4 |
C5 |
1.4 |
0.0 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
| O4 |
C4 |
N3 |
C5 |
179.1 |
180.1 |
| N3 |
C4 |
C5 |
C21 |
181.5 |
180.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
| HN3 |
N3 |
C4 |
O4 |
0.6 |
0.1 |
| HN3 |
N3 |
C4 |
C5 |
181.4 |
180.0 |
| O4 |
C4 |
N3 |
HN3 |
0.6 |
0.1 |
| N3 |
C4 |
O4 |
C5 |
180.9 |
179.9 |
| O4 |
C4 |
C5 |
C21 |
2.3 |
359.9 |
| N1 |
C6 |
C5 |
C4 |
2.9 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
181.4 |
180.0 |
| N3 |
C4 |
C5 |
O4 |
179.1 |
180.1 |
| C6 |
C5 |
C4 |
C21 |
176.2 |
180.0 |
| C4 |
C5 |
C21 |
N23 |
6.0 |
354.3 |
| C4 |
C5 |
C21 |
O22 |
183.3 |
174.3 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
C21 |
183.6 |
180.0 |
| C6 |
C5 |
C21 |
N23 |
189.7 |
174.4 |
| C6 |
C5 |
C21 |
O22 |
7.1 |
354.4 |
| O22 |
C21 |
C5 |
N23 |
177.4 |
180.0 |
| C5 |
C21 |
N23 |
C24 |
176.6 |
185.1 |
| C5 |
C21 |
N23 |
HN23 |
356.6 |
5.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
C21 |
359.3 |
360.0 |
| O4' |
C1' |
C2' |
H1' |
117.5 |
119.6 |
| C2' |
C1' |
O4' |
C4' |
342.8 |
333.5 |
| C3' |
C2' |
C1' |
H2' |
241.2 |
241.4 |
| C3' |
C2' |
C1' |
H2'A |
118.8 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
330.0 |
20.9 |
| C1' |
C2' |
C3' |
H3' |
208.2 |
262.6 |
| H2' |
C2' |
C1' |
H2'A |
237.6 |
237.3 |
| C2' |
C1' |
O4' |
H1' |
243.3 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
28.9 |
2.1 |
| O4' |
C1' |
C2' |
H2' |
147.7 |
120.7 |
| O4' |
C1' |
C2' |
H2'A |
270.0 |
243.3 |
| C1' |
O4' |
C4' |
C5' |
121.3 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
240.7 |
281.5 |
| C2' |
C1' |
H1' |
O4' |
115.2 |
117.9 |
| H1' |
C1' |
C2' |
C3' |
271.4 |
242.4 |
| H1' |
C1' |
C2' |
H2' |
30.2 |
1.1 |
| H1' |
C1' |
C2' |
H2'A |
152.6 |
123.7 |
| H1' |
C1' |
O4' |
C4' |
99.6 |
93.0 |
| C3' |
C2' |
C1' |
O4' |
28.9 |
2.1 |
| C3' |
C2' |
C1' |
H1' |
271.4 |
242.4 |
| C1' |
C2' |
C3' |
H2' |
118.8 |
118.6 |
| C1' |
C2' |
C3' |
H2'A |
241.2 |
241.3 |
| H2' |
C2' |
C3' |
H2'A |
122.4 |
122.6 |
| O3' |
C3' |
C2' |
C4' |
111.1 |
118.2 |
| O3' |
C3' |
C2' |
H3' |
232.9 |
236.4 |
| C4' |
C3' |
C2' |
H3' |
121.8 |
118.2 |
| C2' |
C3' |
C4' |
C5' |
259.8 |
204.5 |
| C2' |
C3' |
C4' |
H4' |
138.6 |
81.6 |
| H2' |
C2' |
C1' |
O4' |
147.7 |
120.7 |
| H2' |
C2' |
C1' |
H1' |
30.2 |
1.1 |
| C1' |
C2' |
H2' |
C3' |
246.9 |
245.3 |
| C1' |
C2' |
H2' |
H2'A |
123.4 |
122.7 |
| C3' |
C2' |
H2' |
H2'A |
236.6 |
237.4 |
| H2' |
C2' |
C3' |
C4' |
211.2 |
262.2 |
| H2' |
C2' |
C3' |
H3' |
89.4 |
144.0 |
| H2'A |
C2' |
C1' |
O4' |
270.0 |
243.3 |
| H2'A |
C2' |
C1' |
H1' |
152.6 |
123.7 |
| C1' |
C2' |
H2'A |
C3' |
113.1 |
114.8 |
| C1' |
C2' |
H2'A |
H2' |
236.6 |
237.4 |
| C3' |
C2' |
H2'A |
H2' |
123.4 |
122.6 |
| H2'A |
C2' |
C3' |
C4' |
88.8 |
139.6 |
| H2'A |
C2' |
C3' |
H3' |
327.0 |
21.4 |
| C5 |
C21 |
N23 |
O22 |
177.2 |
180.0 |
| C24 |
N23 |
C21 |
HN23 |
180.0 |
180.0 |
| C21 |
N23 |
C24 |
C25 |
262.1 |
180.0 |
| C21 |
N23 |
C24 |
H24 |
21.5 |
300.0 |
| C21 |
N23 |
C24 |
H24A |
142.7 |
60.0 |
| C5 |
C21 |
O22 |
N23 |
182.7 |
180.0 |
| O22 |
C21 |
N23 |
C24 |
359.4 |
5.1 |
| O22 |
C21 |
N23 |
HN23 |
179.4 |
185.1 |
| C21 |
N23 |
C24 |
HN23 |
180.0 |
180.0 |
| C25 |
C24 |
N23 |
H24 |
240.6 |
240.0 |
| C25 |
C24 |
N23 |
H24A |
119.4 |
120.0 |
| N23 |
C24 |
C25 |
C26 |
194.3 |
90.0 |
| H24 |
C24 |
N23 |
H24A |
238.9 |
240.0 |
| C21 |
N23 |
HN23 |
C24 |
180.0 |
180.0 |
| HN23 |
N23 |
C24 |
C25 |
82.1 |
360.0 |
| HN23 |
N23 |
C24 |
H24 |
201.5 |
120.0 |
| HN23 |
N23 |
C24 |
H24A |
322.7 |
240.0 |
| C25 |
C24 |
N23 |
HN23 |
82.1 |
360.0 |
| N23 |
C24 |
C25 |
H24 |
119.4 |
120.0 |
| N23 |
C24 |
C25 |
H24A |
240.6 |
240.0 |
| H24 |
C24 |
C25 |
H24A |
121.2 |
120.0 |
| C24 |
C25 |
C26 |
C27 |
179.2 |
180.0 |
| C24 |
C25 |
C26 |
H26 |
359.2 |
360.0 |
| H24 |
C24 |
N23 |
HN23 |
201.5 |
120.0 |
| N23 |
C24 |
H24 |
C25 |
243.4 |
240.0 |
| N23 |
C24 |
H24 |
H24A |
121.7 |
120.0 |
| C25 |
C24 |
H24 |
H24A |
238.3 |
240.0 |
| H24 |
C24 |
C25 |
C26 |
74.8 |
330.0 |
| H24A |
C24 |
N23 |
HN23 |
322.7 |
240.0 |
| N23 |
C24 |
H24A |
C25 |
116.6 |
120.0 |
| N23 |
C24 |
H24A |
H24 |
238.3 |
240.0 |
| C25 |
C24 |
H24A |
H24 |
121.7 |
120.0 |
| H24A |
C24 |
C25 |
C26 |
313.7 |
210.0 |
| C30 |
C25 |
C24 |
H24 |
254.4 |
149.7 |
| C30 |
C25 |
C24 |
H24A |
133.2 |
29.7 |
| C30 |
C25 |
C26 |
H26 |
179.6 |
180.3 |
| C26 |
C25 |
C24 |
H24 |
74.8 |
330.0 |
| C26 |
C25 |
C24 |
H24A |
313.7 |
210.0 |
| C27 |
C26 |
C25 |
H26 |
180.0 |
180.0 |
| C25 |
C26 |
C27 |
H27 |
180.5 |
179.9 |
| C25 |
C26 |
C27 |
H26 |
180.0 |
180.0 |
| C28 |
C27 |
C26 |
H27 |
180.0 |
180.1 |
| C25 |
C26 |
H26 |
C27 |
180.0 |
180.0 |
| H26 |
C26 |
C27 |
H27 |
0.6 |
359.9 |
| C28 |
C27 |
C26 |
H26 |
180.6 |
180.0 |
| C26 |
C27 |
C28 |
H27 |
180.0 |
179.9 |
| H27 |
C27 |
C26 |
H26 |
0.6 |
359.9 |
| C29 |
C28 |
C27 |
H27 |
179.7 |
180.1 |
| H28 |
C28 |
C27 |
H27 |
359.7 |
0.1 |
| C30 |
C29 |
C28 |
H28 |
179.9 |
179.7 |
| H29 |
C29 |
C28 |
H28 |
359.9 |
0.0 |
| O3' |
C3' |
C2' |
H2' |
322.3 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
199.9 |
257.8 |
| C2' |
C3' |
O3' |
C4' |
247.8 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
126.3 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
238.5 |
236.3 |
| O3' |
C3' |
C4' |
C5' |
144.0 |
86.3 |
| O3' |
C3' |
C4' |
H4' |
22.8 |
323.5 |
| C1' |
O4' |
C4' |
C3' |
357.8 |
40.1 |
| C4' |
C3' |
C2' |
H2' |
211.2 |
262.2 |
| C4' |
C3' |
C2' |
H2'A |
88.8 |
139.6 |
| C2' |
C3' |
C4' |
H3' |
238.2 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
122.4 |
123.7 |
| O4' |
C4' |
C3' |
C5' |
121.0 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
242.2 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
121.2 |
122.8 |
| C3' |
C4' |
C5' |
O5' |
44.5 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
164.6 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
284.4 |
65.0 |
| H3' |
C3' |
C2' |
H2' |
89.4 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
327.0 |
21.4 |
| C2' |
C3' |
H3' |
C4' |
117.9 |
112.7 |
| O3' |
C3' |
H3' |
C4' |
243.3 |
236.3 |
| H3' |
C3' |
C4' |
C5' |
21.6 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
260.4 |
199.8 |
| HO3' |
O3' |
C3' |
C4' |
292.2 |
174.1 |
| HO3' |
O3' |
C3' |
H3' |
53.7 |
297.8 |
| H30 |
C30 |
C29 |
H29 |
0.2 |
360.0 |
| C4' |
O4' |
C1' |
H1' |
99.6 |
93.0 |
| O4' |
C4' |
C3' |
H3' |
142.5 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
236.4 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
117.0 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
240.6 |
237.1 |
| O4' |
C4' |
C5' |
O5' |
286.0 |
70.9 |
| O4' |
C4' |
C5' |
H5' |
46.1 |
190.9 |
| O4' |
C4' |
C5' |
H5'A |
165.9 |
310.9 |
| C5' |
C4' |
C3' |
H3' |
21.6 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
238.7 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
120.2 |
123.0 |
| O5' |
C5' |
C4' |
H5' |
239.9 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.1 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
240.2 |
240.0 |
| H4' |
C4' |
C3' |
H3' |
260.4 |
199.8 |
| C3' |
C4' |
H4' |
C5' |
124.5 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
239.7 |
237.0 |
| H4' |
C4' |
C5' |
O5' |
165.8 |
307.9 |
| H4' |
C4' |
C5' |
H5' |
285.9 |
67.9 |
| H4' |
C4' |
C5' |
H5'A |
45.7 |
187.9 |
| C5' |
O5' |
P |
OP2 |
171.5 |
65.0 |
| C5' |
O5' |
P |
OP3 |
287.6 |
185.0 |
| O5' |
C5' |
C4' |
H4' |
165.8 |
307.9 |
| C4' |
C5' |
O5' |
H5' |
120.1 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
239.9 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
119.8 |
119.9 |
| H5' |
C5' |
C4' |
H4' |
285.9 |
67.9 |
| C4' |
C5' |
H5' |
O5' |
239.6 |
240.0 |
| C4' |
C5' |
H5' |
H5'A |
119.8 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
240.2 |
240.1 |
| H5'A |
C5' |
C4' |
H4' |
45.7 |
187.9 |
| C4' |
C5' |
H5'A |
O5' |
120.5 |
120.0 |
| C4' |
C5' |
H5'A |
H5' |
240.2 |
239.9 |
| O5' |
C5' |
H5'A |
H5' |
119.8 |
119.9 |
| HOP2 |
OP2 |
P |
OP3 |
123.4 |
300.0 |