PDB Chemical Component LST
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 LST
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C7 |
C5 |
1.487 |
1.508 |
| OP2 |
P |
1.527 |
1.610 |
| O4 |
C4 |
1.228 |
1.218 |
| P |
OP1 |
1.458 |
1.480 |
| P |
O5' |
1.630 |
1.610 |
| C5 |
C4 |
1.438 |
1.416 |
| C5 |
C6 |
1.346 |
1.351 |
| C4 |
N3 |
1.370 |
1.348 |
| C6 |
N1 |
1.382 |
1.368 |
| O5' |
C5' |
1.439 |
1.430 |
| N3 |
C2 |
1.343 |
1.345 |
| N1 |
C2 |
1.391 |
1.346 |
| N1 |
C1' |
1.471 |
1.465 |
| C5' |
C4' |
1.494 |
1.530 |
| O4' |
C1' |
1.436 |
1.431 |
| O4' |
C4' |
1.457 |
1.435 |
| C2 |
O2 |
1.230 |
1.216 |
| C1' |
C2' |
1.523 |
1.547 |
| C4' |
C3' |
1.535 |
1.547 |
| C4' |
C6' |
1.520 |
1.537 |
| C3' |
C2' |
1.557 |
1.553 |
| C3' |
O3' |
1.437 |
1.429 |
| C6' |
S |
1.769 |
1.820 |
| C2' |
N2' |
1.495 |
1.482 |
| O8' |
S |
1.424 |
1.422 |
| S |
N2' |
1.639 |
1.667 |
| S |
O7' |
1.456 |
1.421 |
| N2' |
C7' |
1.466 |
1.465 |
| C6 |
H1 |
1.080 |
1.079 |
| C1' |
H2 |
1.100 |
1.090 |
| C2' |
H3 |
1.100 |
1.090 |
| C3' |
H4 |
1.100 |
1.090 |
| O3' |
H5 |
0.950 |
0.967 |
| C5' |
H6 |
1.100 |
1.090 |
| C5' |
H7 |
1.100 |
1.090 |
| C6' |
H8 |
1.100 |
1.090 |
| C6' |
H9 |
1.100 |
1.090 |
| OP2 |
H11 |
0.950 |
0.967 |
| C7' |
H12 |
1.100 |
1.090 |
| C7' |
H13 |
1.100 |
1.090 |
| C7' |
H14 |
1.100 |
1.090 |
| C7 |
H15 |
1.100 |
1.090 |
| C7 |
H16 |
1.100 |
1.090 |
| C7 |
H17 |
1.100 |
1.090 |
| N3 |
H18 |
1.000 |
0.971 |
| P |
OP3 |
1.609 |
1.610 |
| OP3 |
H10 |
0.950 |
0.966 |
Bond Angles for LST
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
110.7 |
109.5 |
| OP1 |
P |
OP3 |
104.7 |
109.5 |
| C5 |
C4 |
N3 |
115.5 |
119.4 |
| C5 |
C6 |
N1 |
121.7 |
119.7 |
| C5 |
C6 |
H1 |
119.2 |
120.1 |
| C4 |
N3 |
H18 |
116.4 |
119.9 |
| C6 |
N1 |
C1' |
124.1 |
119.7 |
| N1 |
C6 |
H1 |
119.1 |
120.2 |
| O5' |
C5' |
H6 |
110.5 |
109.5 |
| O5' |
C5' |
H7 |
110.5 |
109.5 |
| N3 |
C2 |
O2 |
123.0 |
119.6 |
| N1 |
C2 |
O2 |
121.6 |
119.5 |
| N1 |
C1' |
H2 |
110.6 |
109.8 |
| C5' |
C4' |
C6' |
108.0 |
111.3 |
| O4' |
C1' |
H2 |
111.1 |
109.9 |
| C1' |
C2' |
N2' |
113.6 |
106.4 |
| C2' |
C1' |
H2 |
109.9 |
109.8 |
| C1' |
C2' |
H3 |
109.6 |
113.5 |
| C4' |
C3' |
H4 |
110.5 |
111.1 |
| C4' |
C6' |
S |
114.7 |
108.4 |
| C4' |
C6' |
H8 |
108.2 |
109.7 |
| C4' |
C6' |
H9 |
108.1 |
109.7 |
| C3' |
C2' |
N2' |
114.5 |
106.2 |
| C3' |
C2' |
H3 |
109.2 |
114.4 |
| O3' |
C3' |
H4 |
111.9 |
110.9 |
| C3' |
O3' |
H5 |
109.5 |
114.0 |
| C6' |
S |
N2' |
104.5 |
103.1 |
| C6' |
S |
O7' |
109.1 |
110.8 |
| S |
C6' |
H8 |
108.2 |
109.7 |
| S |
C6' |
H9 |
108.2 |
109.7 |
| C2' |
N2' |
C7' |
116.2 |
121.8 |
| N2' |
C2' |
H3 |
110.0 |
113.4 |
| N2' |
C7' |
H12 |
109.5 |
109.5 |
| N2' |
C7' |
H13 |
109.5 |
109.5 |
| N2' |
C7' |
H14 |
109.4 |
109.5 |
| H6 |
C5' |
H7 |
109.5 |
109.5 |
| H8 |
C6' |
H9 |
109.5 |
109.7 |
| H12 |
C7' |
H13 |
109.4 |
109.4 |
| H12 |
C7' |
H14 |
109.5 |
109.5 |
| H13 |
C7' |
H14 |
109.5 |
109.5 |
| H15 |
C7 |
H16 |
109.5 |
109.5 |
| H15 |
C7 |
H17 |
109.4 |
109.5 |
| H16 |
C7 |
H17 |
109.5 |
109.5 |
| P |
OP3 |
H10 |
109.5 |
114.1 |
Torsion Angles for LST
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7 |
C5 |
C4 |
N3 |
178.4 |
180.0 |
| C7 |
C5 |
C6 |
H1 |
0.9 |
0.2 |
| OP1 |
P |
OP2 |
OP3 |
237.6 |
240.0 |
| OP2 |
P |
OP3 |
H10 |
228.9 |
300.0 |
| O4 |
C4 |
N3 |
H18 |
358.8 |
360.0 |
| OP2 |
P |
OP1 |
OP3 |
125.3 |
120.0 |
| OP1 |
P |
OP3 |
H10 |
360.0 |
60.0 |
| P |
O5' |
C5' |
H6 |
295.9 |
60.0 |
| P |
O5' |
C5' |
H7 |
57.3 |
300.0 |
| C5 |
C4 |
N3 |
H18 |
179.8 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
358.8 |
0.2 |
| C5 |
C6 |
N1 |
C1' |
182.4 |
180.0 |
| N1 |
C6 |
C5 |
H1 |
180.0 |
179.8 |
| C4 |
N3 |
C2 |
O2 |
181.6 |
180.0 |
| C5 |
C6 |
N1 |
H1 |
180.0 |
180.2 |
| C6 |
N1 |
C2 |
O2 |
177.7 |
180.0 |
| C6 |
N1 |
C1' |
H2 |
140.8 |
144.9 |
| O5' |
C5' |
C4' |
C6' |
176.0 |
305.1 |
| H6 |
C5' |
O5' |
H7 |
238.6 |
120.0 |
| N1 |
C2 |
N3 |
O2 |
180.7 |
179.7 |
| N3 |
C2 |
N1 |
O2 |
179.3 |
180.3 |
| C1' |
N1 |
C6 |
H1 |
2.4 |
359.8 |
| C1' |
N1 |
C2 |
O2 |
357.1 |
360.0 |
| O4' |
C1' |
N1 |
H2 |
238.4 |
239.0 |
| C2' |
C1' |
N1 |
H2 |
123.1 |
120.9 |
| N1 |
C1' |
C2' |
H3 |
329.3 |
333.7 |
| C5' |
C4' |
C3' |
H4 |
310.3 |
321.1 |
| C5' |
C4' |
C6' |
S |
172.2 |
172.9 |
| C5' |
C4' |
C6' |
H8 |
293.0 |
292.7 |
| C5' |
C4' |
C6' |
H9 |
51.4 |
53.2 |
| C6 |
N1 |
C1' |
O4' |
19.2 |
23.9 |
| N1 |
C1' |
O4' |
H2 |
121.3 |
121.0 |
| C2' |
C1' |
O4' |
H2 |
241.1 |
240.5 |
| O4' |
C1' |
C2' |
H3 |
212.5 |
214.1 |
| C4' |
O4' |
C1' |
H2 |
124.6 |
119.8 |
| O4' |
C4' |
C3' |
H4 |
71.7 |
82.9 |
| O4' |
C4' |
C6' |
H8 |
170.4 |
168.7 |
| O4' |
C4' |
C6' |
H9 |
288.8 |
289.2 |
| C6 |
N1 |
C1' |
C2' |
263.9 |
265.8 |
| N1 |
C1' |
C2' |
H2 |
236.5 |
239.1 |
| O4' |
C1' |
C2' |
H2 |
119.7 |
119.6 |
| C3' |
C2' |
C1' |
N2' |
238.0 |
248.9 |
| C3' |
C2' |
C1' |
H3 |
114.4 |
123.6 |
| C1' |
C2' |
N2' |
C7' |
85.3 |
137.0 |
| N2' |
C2' |
C1' |
H3 |
236.5 |
234.6 |
| C4' |
C3' |
C2' |
N2' |
285.5 |
282.7 |
| C4' |
C3' |
C2' |
H3 |
161.7 |
156.9 |
| O3' |
C3' |
C4' |
H4 |
124.4 |
124.0 |
| C4' |
C3' |
O3' |
H5 |
180.0 |
173.4 |
| C6' |
C4' |
C3' |
H4 |
187.9 |
198.8 |
| C4' |
C6' |
S |
N2' |
38.7 |
43.7 |
| C4' |
C6' |
S |
O7' |
151.0 |
155.0 |
| S |
C6' |
C4' |
H8 |
239.2 |
240.2 |
| S |
C6' |
C4' |
H9 |
120.8 |
119.7 |
| H8 |
C6' |
C4' |
H9 |
241.6 |
239.5 |
| C1' |
C2' |
C3' |
N2' |
121.4 |
111.2 |
| C3' |
C2' |
C1' |
H2 |
207.2 |
218.1 |
| C1' |
C2' |
C3' |
H3 |
245.3 |
237.0 |
| C3' |
C2' |
N2' |
C7' |
198.5 |
245.1 |
| N2' |
C2' |
C3' |
H3 |
123.8 |
125.8 |
| C4' |
C3' |
O3' |
H4 |
236.4 |
235.9 |
| O3' |
C3' |
C2' |
N2' |
42.9 |
40.8 |
| O3' |
C3' |
C2' |
H3 |
279.1 |
275.0 |
| C4' |
C6' |
S |
H8 |
120.8 |
119.8 |
| C4' |
C6' |
S |
H9 |
239.2 |
240.3 |
| H8 |
C6' |
S |
H9 |
118.5 |
120.5 |
| N2' |
C2' |
C1' |
H2 |
329.2 |
329.2 |
| C1' |
C2' |
N2' |
H3 |
123.3 |
125.5 |
| C3' |
C2' |
N2' |
H3 |
236.6 |
233.6 |
| C6' |
S |
N2' |
C2' |
323.1 |
314.2 |
| C2' |
N2' |
C7' |
H12 |
222.6 |
90.0 |
| C2' |
N2' |
C7' |
H13 |
342.6 |
210.0 |
| C2' |
N2' |
C7' |
H14 |
102.6 |
330.0 |
| O8' |
S |
C6' |
H8 |
160.7 |
172.7 |
| O8' |
S |
C6' |
H9 |
42.3 |
52.2 |
| C6' |
S |
N2' |
O7' |
114.9 |
115.9 |
| N2' |
S |
C6' |
H8 |
277.9 |
283.9 |
| N2' |
S |
C6' |
H9 |
159.4 |
163.4 |
| S |
N2' |
C2' |
H3 |
184.2 |
191.5 |
| S |
N2' |
C7' |
H12 |
0.0 |
270.1 |
| S |
N2' |
C7' |
H13 |
120.0 |
30.0 |
| S |
N2' |
C7' |
H14 |
240.0 |
150.0 |
| C6' |
S |
O7' |
N2' |
248.3 |
249.6 |
| O7' |
S |
C6' |
H8 |
30.2 |
35.2 |
| O7' |
S |
C6' |
H9 |
271.7 |
274.7 |
| C6' |
S |
N2' |
C7' |
184.9 |
134.1 |
| C7' |
N2' |
C2' |
H3 |
321.9 |
11.6 |
| H12 |
C7' |
N2' |
H13 |
240.0 |
240.0 |
| H12 |
C7' |
N2' |
H14 |
120.0 |
120.0 |
| H13 |
C7' |
N2' |
H14 |
240.0 |
240.0 |
| C5 |
C6 |
H1 |
N1 |
180.0 |
179.8 |
| H1 |
C6 |
N1 |
C1' |
2.4 |
359.8 |
| H2 |
C1' |
C2' |
N2' |
329.2 |
329.2 |
| H2 |
C1' |
C2' |
H3 |
92.8 |
94.6 |
| C1' |
C2' |
H3 |
N2' |
234.3 |
238.5 |
| H3 |
C2' |
C1' |
H2 |
92.8 |
94.6 |
| C3' |
C2' |
H3 |
N2' |
126.4 |
122.0 |
| H3 |
C2' |
N2' |
C7' |
321.9 |
11.6 |
| H4 |
C3' |
C2' |
N2' |
169.6 |
164.6 |
| H4 |
C3' |
C2' |
H3 |
45.7 |
38.8 |
| H4 |
C3' |
O3' |
H5 |
303.6 |
297.5 |
| H5 |
O3' |
C3' |
H4 |
303.6 |
297.5 |
| O5' |
C5' |
H6 |
H7 |
122.0 |
240.0 |
| H6 |
C5' |
C4' |
C6' |
56.7 |
65.1 |
| O5' |
C5' |
H7 |
H6 |
238.0 |
120.0 |
| H7 |
C5' |
C4' |
C6' |
295.4 |
185.1 |
| C4' |
C6' |
H8 |
S |
235.2 |
241.0 |
| C4' |
C6' |
H8 |
H9 |
117.6 |
120.5 |
| H8 |
C6' |
S |
N2' |
277.9 |
283.9 |
| H8 |
C6' |
S |
O7' |
30.2 |
35.2 |
| S |
C6' |
H8 |
H9 |
242.4 |
239.5 |
| C4' |
C6' |
H9 |
S |
124.7 |
119.0 |
| C4' |
C6' |
H9 |
H8 |
242.4 |
239.4 |
| H9 |
C6' |
S |
N2' |
159.4 |
163.4 |
| H9 |
C6' |
S |
O7' |
271.7 |
274.7 |
| S |
C6' |
H9 |
H8 |
117.6 |
120.5 |
| H11 |
OP2 |
P |
OP3 |
122.4 |
300.0 |
| N2' |
C7' |
H12 |
H13 |
120.0 |
120.0 |
| N2' |
C7' |
H12 |
H14 |
240.0 |
240.0 |
| H13 |
C7' |
H12 |
H14 |
120.0 |
120.0 |
| N2' |
C7' |
H13 |
H12 |
240.0 |
240.0 |
| N2' |
C7' |
H13 |
H14 |
120.0 |
120.0 |
| H12 |
C7' |
H13 |
H14 |
240.0 |
240.0 |
| N2' |
C7' |
H14 |
H12 |
120.0 |
120.1 |
| N2' |
C7' |
H14 |
H13 |
240.0 |
240.0 |
| H12 |
C7' |
H14 |
H13 |
120.0 |
120.0 |
| H16 |
C7 |
H15 |
H17 |
120.0 |
120.1 |
| H15 |
C7 |
H16 |
H17 |
240.1 |
239.9 |
| H15 |
C7 |
H17 |
H16 |
120.0 |
120.1 |
| H18 |
N3 |
C2 |
O2 |
1.6 |
0.0 |