PDB Chemical Component PRT
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 PRT
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O13 |
C13 |
1.438 |
1.428 |
| O1P |
P |
1.584 |
1.480 |
| C13 |
C14 |
1.517 |
1.541 |
| C13 |
C12 |
1.527 |
1.549 |
| C14 |
C15 |
1.534 |
1.531 |
| C14 |
O14 |
1.442 |
1.439 |
| C15 |
O15 |
1.433 |
1.429 |
| O12 |
C12 |
1.429 |
1.429 |
| C12 |
C11 |
1.478 |
1.550 |
| P |
O15 |
1.606 |
1.610 |
| P |
O2P |
1.483 |
1.610 |
| P |
O3P |
1.589 |
1.610 |
| O1B |
PB |
1.607 |
1.480 |
| O14 |
C11 |
1.463 |
1.443 |
| C11 |
N1 |
1.480 |
1.466 |
| O2G |
PG |
1.587 |
1.480 |
| O2A |
PA |
1.488 |
1.480 |
| O2B |
PB |
1.471 |
1.610 |
| PB |
O3B |
1.615 |
1.610 |
| PB |
O3A |
1.576 |
1.610 |
| O3G |
PG |
1.481 |
1.610 |
| N1 |
C2 |
1.394 |
1.363 |
| N1 |
C6 |
1.354 |
1.397 |
| PG |
O3B |
1.625 |
1.610 |
| PG |
O1G |
1.682 |
1.610 |
| C2 |
N3 |
1.365 |
1.310 |
| N6 |
C6 |
1.333 |
1.312 |
| PA |
O3A |
1.523 |
1.610 |
| PA |
O1A |
1.558 |
1.610 |
| PA |
O5' |
1.624 |
1.610 |
| C6 |
C5 |
1.351 |
1.474 |
| N3 |
C4 |
1.339 |
1.345 |
| O5' |
C5' |
1.422 |
1.429 |
| C5 |
C4 |
1.349 |
1.407 |
| C5 |
N7 |
1.331 |
1.333 |
| C4 |
N9 |
1.322 |
1.356 |
| N7 |
C8 |
1.335 |
1.308 |
| C5' |
C4' |
1.526 |
1.530 |
| C3' |
O3' |
1.402 |
1.429 |
| C3' |
C4' |
1.521 |
1.541 |
| C3' |
C2' |
1.549 |
1.548 |
| N9 |
C8 |
1.338 |
1.367 |
| N9 |
C1' |
1.518 |
1.465 |
| C4' |
O4' |
1.456 |
1.437 |
| O4' |
C1' |
1.431 |
1.444 |
| C2' |
C1' |
1.502 |
1.550 |
| C2' |
O2' |
1.419 |
1.429 |
| O1G |
H1 |
0.950 |
0.967 |
| O3G |
H2 |
0.949 |
0.967 |
| O2B |
H3 |
0.950 |
0.967 |
| O1A |
H4 |
0.950 |
0.967 |
| C5' |
H5 |
1.100 |
1.090 |
| C5' |
H6 |
1.100 |
1.090 |
| C4' |
H7 |
1.100 |
1.090 |
| C3' |
H8 |
1.100 |
1.090 |
| O3' |
H9 |
0.950 |
0.967 |
| C2' |
H10 |
1.100 |
1.090 |
| O2' |
H11 |
0.951 |
0.968 |
| C1' |
H12 |
1.100 |
1.090 |
| C8 |
H13 |
1.080 |
1.080 |
| N6 |
H14 |
1.001 |
0.971 |
| C2 |
H16 |
1.080 |
1.079 |
| C11 |
H17 |
1.100 |
1.090 |
| C12 |
H18 |
1.100 |
1.090 |
| O12 |
H19 |
0.950 |
0.968 |
| C13 |
H20 |
1.100 |
1.090 |
| O13 |
H21 |
0.950 |
0.967 |
| C14 |
H22 |
1.100 |
1.090 |
| C15 |
H23 |
1.100 |
1.090 |
| C15 |
H24 |
1.100 |
1.090 |
| O3P |
H25 |
0.950 |
0.968 |
| O2P |
H26 |
0.950 |
0.967 |
Bond Angles for PRT
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O13 |
C13 |
C14 |
106.8 |
110.5 |
| O13 |
C13 |
H20 |
112.4 |
110.6 |
| O1P |
P |
O2P |
116.1 |
109.4 |
| C13 |
C14 |
C15 |
112.8 |
109.9 |
| C13 |
C14 |
O14 |
105.7 |
107.4 |
| C14 |
C13 |
H20 |
111.2 |
110.5 |
| C13 |
C14 |
H22 |
109.5 |
109.9 |
| C13 |
C12 |
H18 |
112.3 |
110.9 |
| C14 |
C15 |
O15 |
110.6 |
109.5 |
| C15 |
C14 |
H22 |
109.3 |
109.9 |
| C14 |
C15 |
H23 |
109.2 |
109.4 |
| C14 |
C15 |
H24 |
109.2 |
109.4 |
| O15 |
C15 |
H23 |
109.2 |
109.5 |
| O15 |
C15 |
H24 |
109.2 |
109.5 |
| O12 |
C12 |
H18 |
113.9 |
110.8 |
| C12 |
C11 |
H17 |
109.3 |
110.6 |
| O3P |
P |
O2P |
108.3 |
109.5 |
| P |
O2P |
H26 |
109.5 |
114.0 |
| P |
O3P |
H25 |
109.5 |
114.0 |
| O1B |
PB |
O3A |
112.7 |
109.4 |
| O14 |
C11 |
H17 |
109.5 |
110.7 |
| O2G |
PG |
O3B |
101.3 |
109.5 |
| O2A |
PA |
O5' |
113.6 |
109.5 |
| O2B |
PB |
O3A |
102.4 |
109.5 |
| O3G |
PG |
O3B |
111.6 |
109.5 |
| N1 |
C2 |
H16 |
120.3 |
118.3 |
| PG |
O1G |
H1 |
109.5 |
114.0 |
| O1A |
PA |
O5' |
104.1 |
109.5 |
| PA |
O1A |
H4 |
109.5 |
114.0 |
| PA |
O5' |
C5' |
121.7 |
123.0 |
| O5' |
C5' |
C4' |
107.0 |
109.5 |
| O5' |
C5' |
H5 |
110.1 |
109.5 |
| O5' |
C5' |
H6 |
110.1 |
109.5 |
| N7 |
C8 |
H13 |
125.5 |
125.2 |
| C5' |
C4' |
O4' |
109.6 |
109.9 |
| C4' |
C5' |
H5 |
110.1 |
109.5 |
| C4' |
C5' |
H6 |
110.1 |
109.4 |
| C5' |
C4' |
H7 |
108.9 |
109.9 |
| O3' |
C3' |
C2' |
111.0 |
110.5 |
| O3' |
C3' |
H8 |
113.2 |
110.4 |
| C3' |
O3' |
H9 |
109.5 |
114.0 |
| C3' |
C4' |
H7 |
109.0 |
110.0 |
| C3' |
C2' |
C1' |
103.6 |
102.1 |
| C3' |
C2' |
O2' |
109.9 |
110.9 |
| C2' |
C3' |
H8 |
110.9 |
110.6 |
| C3' |
C2' |
H10 |
110.1 |
110.9 |
| N9 |
C8 |
H13 |
125.6 |
125.1 |
| N9 |
C1' |
H12 |
109.4 |
110.6 |
| C4' |
O4' |
C1' |
108.7 |
107.0 |
| O4' |
C4' |
H7 |
109.9 |
109.9 |
| O4' |
C1' |
C2' |
106.6 |
103.5 |
| O4' |
C1' |
H12 |
110.6 |
110.7 |
| O2' |
C2' |
C1' |
110.0 |
110.9 |
| C1' |
C2' |
H10 |
110.8 |
110.9 |
| C2' |
C1' |
H12 |
109.6 |
110.6 |
| O2' |
C2' |
H10 |
112.1 |
110.8 |
| C2' |
O2' |
H11 |
109.5 |
114.0 |
| H5 |
C5' |
H6 |
109.4 |
109.4 |
| H23 |
C15 |
H24 |
109.4 |
109.5 |
Torsion Angles for PRT
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O13 |
C13 |
C14 |
C15 |
142.8 |
119.7 |
| O13 |
C13 |
C14 |
O14 |
261.7 |
239.3 |
| C14 |
C13 |
O13 |
H20 |
237.7 |
237.4 |
| O13 |
C13 |
C14 |
H22 |
20.8 |
358.7 |
| O13 |
C13 |
C12 |
H18 |
197.4 |
216.0 |
| O3P |
P |
O1P |
O2P |
240.0 |
240.0 |
| O1P |
P |
O2P |
H26 |
360.0 |
180.0 |
| O1P |
P |
O3P |
H25 |
360.0 |
59.9 |
| O13 |
C13 |
C14 |
H20 |
123.0 |
122.7 |
| C14 |
C13 |
C12 |
H18 |
82.9 |
97.3 |
| C13 |
C14 |
C15 |
O15 |
48.9 |
185.0 |
| C15 |
C14 |
C13 |
H22 |
122.0 |
121.0 |
| C13 |
C14 |
C15 |
H23 |
169.0 |
305.0 |
| C13 |
C14 |
C15 |
H24 |
288.7 |
65.0 |
| O12 |
C12 |
C13 |
H18 |
127.6 |
123.6 |
| C13 |
C12 |
C11 |
H17 |
284.8 |
278.3 |
| C13 |
C14 |
C15 |
O14 |
117.0 |
118.0 |
| C15 |
C14 |
C13 |
H20 |
19.7 |
357.0 |
| C13 |
C14 |
C15 |
H22 |
237.9 |
239.0 |
| O15 |
C15 |
C14 |
H23 |
239.8 |
240.0 |
| O15 |
C15 |
C14 |
H24 |
120.2 |
120.0 |
| H23 |
C15 |
C14 |
H24 |
240.4 |
240.0 |
| C13 |
C14 |
O14 |
C15 |
238.5 |
240.5 |
| O14 |
C14 |
C13 |
H20 |
138.7 |
116.6 |
| C13 |
C14 |
O14 |
H22 |
118.4 |
119.5 |
| C14 |
O14 |
C11 |
H17 |
85.0 |
78.8 |
| O15 |
C15 |
C14 |
H22 |
170.9 |
306.0 |
| C14 |
C15 |
O15 |
H23 |
120.2 |
120.0 |
| C14 |
C15 |
O15 |
H24 |
239.8 |
240.0 |
| H23 |
C15 |
O15 |
H24 |
119.7 |
120.1 |
| C13 |
C12 |
O12 |
H18 |
233.3 |
236.4 |
| O12 |
C12 |
C11 |
H17 |
38.9 |
36.6 |
| O14 |
C11 |
C12 |
H17 |
117.4 |
118.6 |
| P |
O15 |
C15 |
H23 |
82.9 |
60.0 |
| P |
O15 |
C15 |
H24 |
323.3 |
300.0 |
| O2P |
P |
O3P |
H25 |
234.9 |
300.0 |
| O1P |
P |
O3P |
O2P |
125.1 |
120.0 |
| O3P |
P |
O2P |
H26 |
118.7 |
300.0 |
| O2B |
PB |
O1B |
O3A |
115.1 |
120.0 |
| C12 |
C11 |
O14 |
H17 |
242.7 |
241.4 |
| C11 |
N1 |
C2 |
H16 |
356.8 |
336.0 |
| O3G |
PG |
O2G |
O3B |
118.8 |
120.0 |
| O2G |
PG |
O1G |
H1 |
0.0 |
180.0 |
| O1A |
PA |
O2A |
O5' |
241.3 |
240.0 |
| O2A |
PA |
O1A |
H4 |
0.0 |
180.0 |
| O2A |
PA |
O5' |
C5' |
179.6 |
305.0 |
| O1B |
PB |
O2B |
O3A |
238.8 |
240.0 |
| O2G |
PG |
O3G |
O3B |
247.6 |
240.0 |
| O3G |
PG |
O1G |
H1 |
127.2 |
300.0 |
| O3B |
PG |
O1G |
H1 |
250.8 |
60.0 |
| O2A |
PA |
O1A |
O5' |
124.0 |
120.0 |
| O1A |
PA |
O5' |
C5' |
303.5 |
65.0 |
| O5' |
PA |
O1A |
H4 |
236.0 |
60.0 |
| PA |
O5' |
C5' |
C4' |
187.7 |
180.0 |
| PA |
O5' |
C5' |
H5 |
307.4 |
300.0 |
| PA |
O5' |
C5' |
H6 |
68.1 |
60.1 |
| O5' |
C5' |
C4' |
O4' |
293.8 |
66.5 |
| C4' |
C5' |
O5' |
H5 |
240.4 |
240.0 |
| C4' |
C5' |
O5' |
H6 |
119.6 |
119.9 |
| O5' |
C5' |
C4' |
H7 |
173.5 |
305.5 |
| H5 |
C5' |
O5' |
H6 |
239.3 |
240.0 |
| C5 |
N7 |
C8 |
H13 |
180.6 |
179.6 |
| C4 |
N9 |
C8 |
H13 |
179.5 |
180.3 |
| C4 |
N9 |
C1' |
H12 |
182.5 |
326.3 |
| N9 |
C8 |
N7 |
H13 |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5 |
119.6 |
120.1 |
| O5' |
C5' |
C4' |
H6 |
240.4 |
240.0 |
| C3' |
C4' |
C5' |
H7 |
236.2 |
238.8 |
| C5' |
C4' |
O4' |
C1' |
157.9 |
145.9 |
| O4' |
C4' |
C5' |
H7 |
120.3 |
121.0 |
| H5 |
C5' |
C4' |
H6 |
120.7 |
119.9 |
| O3' |
C3' |
C4' |
H7 |
317.2 |
358.8 |
| O3' |
C3' |
C2' |
C1' |
153.5 |
97.8 |
| O3' |
C3' |
C2' |
O2' |
36.0 |
339.6 |
| C2' |
C3' |
O3' |
H8 |
125.5 |
122.7 |
| O3' |
C3' |
C2' |
H10 |
272.1 |
216.0 |
| C3' |
C4' |
C5' |
H5 |
290.1 |
64.2 |
| C3' |
C4' |
C5' |
H6 |
169.3 |
304.3 |
| C5' |
C4' |
C3' |
H7 |
123.7 |
121.1 |
| C3' |
C4' |
O4' |
C1' |
33.5 |
26.5 |
| O4' |
C4' |
C3' |
H7 |
243.5 |
240.5 |
| O3' |
C3' |
C2' |
H8 |
233.2 |
237.4 |
| C2' |
C3' |
O3' |
H9 |
71.0 |
65.2 |
| C2' |
C3' |
C4' |
H7 |
73.8 |
117.5 |
| O4' |
C1' |
C2' |
C3' |
341.3 |
37.0 |
| O2' |
C2' |
C3' |
C1' |
242.5 |
241.8 |
| C1' |
C2' |
C3' |
H10 |
241.5 |
241.7 |
| C3' |
C2' |
C1' |
H12 |
221.6 |
278.5 |
| O2' |
C2' |
C3' |
H10 |
124.0 |
123.6 |
| C3' |
C2' |
O2' |
H11 |
180.0 |
298.5 |
| N7 |
C8 |
N9 |
H13 |
180.0 |
180.0 |
| C8 |
N9 |
C1' |
H12 |
1.8 |
146.6 |
| O4' |
C1' |
N9 |
H12 |
240.3 |
237.0 |
| N9 |
C1' |
C2' |
H10 |
340.7 |
37.3 |
| C2' |
C1' |
N9 |
H12 |
123.0 |
122.9 |
| O4' |
C4' |
C5' |
H5 |
174.1 |
306.4 |
| O4' |
C4' |
C5' |
H6 |
53.4 |
186.5 |
| C5' |
C4' |
O4' |
H7 |
240.3 |
239.0 |
| C3' |
C4' |
O4' |
H7 |
115.9 |
119.6 |
| C4' |
O4' |
C1' |
C2' |
351.0 |
319.9 |
| C4' |
O4' |
C1' |
H12 |
110.1 |
78.4 |
| C3' |
C2' |
C1' |
O4' |
341.3 |
37.0 |
| N9 |
C1' |
O4' |
H12 |
118.9 |
123.0 |
| C1' |
O4' |
C4' |
H7 |
277.6 |
266.9 |
| O2' |
C2' |
C1' |
O4' |
98.7 |
155.2 |
| O4' |
C1' |
C2' |
H10 |
223.2 |
278.8 |
| C2' |
C1' |
O4' |
H12 |
240.9 |
241.5 |
| C3' |
C2' |
C1' |
O2' |
242.5 |
241.8 |
| C1' |
C2' |
C3' |
H8 |
280.3 |
220.4 |
| C3' |
C2' |
C1' |
H10 |
118.1 |
118.2 |
| N9 |
C1' |
C2' |
H12 |
237.2 |
237.1 |
| O4' |
C1' |
C2' |
H12 |
119.7 |
118.6 |
| O2' |
C2' |
C1' |
H10 |
235.5 |
236.4 |
| C1' |
C2' |
O2' |
H11 |
66.6 |
185.8 |
| C3' |
C2' |
O2' |
C1' |
113.4 |
112.7 |
| O2' |
C2' |
C3' |
H8 |
162.8 |
102.2 |
| C3' |
C2' |
O2' |
H10 |
237.2 |
236.4 |
| O4' |
C1' |
C2' |
O2' |
98.7 |
155.2 |
| C1' |
C2' |
O2' |
H10 |
123.8 |
123.7 |
| O2' |
C2' |
C1' |
H12 |
339.0 |
36.6 |
| H2 |
O3G |
PG |
O3B |
112.4 |
180.0 |
| H3 |
O2B |
PB |
O3A |
121.2 |
300.0 |
| H4 |
O1A |
PA |
O5' |
236.0 |
60.0 |
| O5' |
C5' |
H5 |
C4' |
242.3 |
240.0 |
| O5' |
C5' |
H5 |
H6 |
121.1 |
120.0 |
| H5 |
C5' |
C4' |
O4' |
174.1 |
306.4 |
| C4' |
C5' |
H5 |
H6 |
238.9 |
240.1 |
| H5 |
C5' |
C4' |
H7 |
53.8 |
185.4 |
| O5' |
C5' |
H6 |
C4' |
117.7 |
120.0 |
| O5' |
C5' |
H6 |
H5 |
238.9 |
239.9 |
| H6 |
C5' |
C4' |
O4' |
53.4 |
186.5 |
| C4' |
C5' |
H6 |
H5 |
121.1 |
120.0 |
| H6 |
C5' |
C4' |
H7 |
293.1 |
65.4 |
| C5' |
C4' |
H7 |
O4' |
120.1 |
121.0 |
| H7 |
C4' |
C5' |
H5 |
53.8 |
185.4 |
| H7 |
C4' |
C5' |
H6 |
293.1 |
65.4 |
| H7 |
C4' |
O4' |
C1' |
277.6 |
266.9 |
| O3' |
C3' |
H8 |
C2' |
125.6 |
122.7 |
| H8 |
C3' |
O3' |
H9 |
305.5 |
302.5 |
| H8 |
C3' |
C4' |
H7 |
190.6 |
236.3 |
| H8 |
C3' |
C2' |
C1' |
280.3 |
220.4 |
| H8 |
C3' |
C2' |
O2' |
162.8 |
102.2 |
| H8 |
C3' |
C2' |
H10 |
38.9 |
338.7 |
| H9 |
O3' |
C3' |
C2' |
71.0 |
65.2 |
| H9 |
O3' |
C3' |
H8 |
305.5 |
302.5 |
| C3' |
C2' |
H10 |
C1' |
246.0 |
247.2 |
| C3' |
C2' |
H10 |
O2' |
122.7 |
123.6 |
| H10 |
C2' |
C3' |
H8 |
38.9 |
338.7 |
| O2' |
C2' |
H10 |
C1' |
123.3 |
123.7 |
| H10 |
C2' |
C1' |
H12 |
103.5 |
160.2 |
| H10 |
C2' |
O2' |
H11 |
302.8 |
62.2 |
| H11 |
O2' |
C2' |
C1' |
66.6 |
185.8 |
| H11 |
O2' |
C2' |
H10 |
302.8 |
62.2 |
| O4' |
C1' |
H12 |
C2' |
242.8 |
245.9 |
| H12 |
C1' |
C2' |
H10 |
103.5 |
160.2 |
| H18 |
C12 |
C11 |
H17 |
165.5 |
160.2 |
| H19 |
O12 |
C12 |
H18 |
306.7 |
56.4 |
| O13 |
C13 |
H20 |
C14 |
240.3 |
237.3 |
| H20 |
C13 |
C14 |
C15 |
19.7 |
357.0 |
| H20 |
C13 |
C14 |
O14 |
138.7 |
116.6 |
| H20 |
C13 |
C14 |
H22 |
257.8 |
236.0 |
| H20 |
C13 |
C12 |
H18 |
322.9 |
338.7 |
| H21 |
O13 |
C13 |
C14 |
180.0 |
180.0 |
| H21 |
O13 |
C13 |
H20 |
302.3 |
302.6 |
| C13 |
C14 |
H22 |
C15 |
124.1 |
121.0 |
| C13 |
C14 |
H22 |
O14 |
244.0 |
242.1 |
| H22 |
C14 |
C13 |
H20 |
257.8 |
236.0 |
| H22 |
C14 |
C15 |
O15 |
170.9 |
306.0 |
| H22 |
C14 |
C15 |
H23 |
291.1 |
66.0 |
| H22 |
C14 |
C15 |
H24 |
50.8 |
186.0 |
| C14 |
C15 |
H23 |
O15 |
239.0 |
240.0 |
| H23 |
C15 |
C14 |
H22 |
291.1 |
66.0 |
| C14 |
C15 |
H23 |
H24 |
119.5 |
119.9 |
| O15 |
C15 |
H23 |
H24 |
240.5 |
239.9 |
| C14 |
C15 |
H24 |
O15 |
121.0 |
120.0 |
| H24 |
C15 |
C14 |
H22 |
50.8 |
186.0 |
| C14 |
C15 |
H24 |
H23 |
240.5 |
240.1 |
| O15 |
C15 |
H24 |
H23 |
119.5 |
120.1 |
| H25 |
O3P |
P |
O2P |
234.9 |
300.0 |