PDB Chemical Component JSP
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 JSP
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.430 |
1.430 |
| O5' |
P |
1.605 |
1.610 |
| O5' |
C5' |
1.431 |
1.429 |
| C3' |
C4' |
1.531 |
1.541 |
| C3' |
C2' |
1.528 |
1.548 |
| OP2 |
P |
1.481 |
1.610 |
| OP1 |
P |
1.481 |
1.480 |
| C4' |
C5' |
1.526 |
1.530 |
| C4' |
O4' |
1.455 |
1.439 |
| C2' |
C1' |
1.520 |
1.549 |
| O4' |
C1' |
1.417 |
1.444 |
| C1' |
C1 |
1.564 |
1.507 |
| C1 |
C6 |
1.338 |
1.354 |
| C1 |
C2 |
1.349 |
1.410 |
| C6 |
N5 |
1.349 |
1.362 |
| N2 |
C2 |
1.269 |
1.375 |
| C2 |
N3 |
1.268 |
1.327 |
| N5 |
C7 |
1.461 |
1.465 |
| N5 |
C4 |
1.376 |
1.346 |
| N3 |
C4 |
1.271 |
1.332 |
| C4 |
O4 |
1.213 |
1.220 |
| C1' |
H1 |
1.100 |
1.090 |
| C2' |
H2 |
1.100 |
1.090 |
| C2' |
H3 |
1.099 |
1.091 |
| C3' |
H4 |
1.100 |
1.090 |
| C4' |
H5 |
1.100 |
1.091 |
| C5' |
H6 |
1.100 |
1.089 |
| C5' |
H7 |
1.099 |
1.090 |
| C6 |
H8 |
1.080 |
1.080 |
| C7 |
H9 |
1.100 |
1.090 |
| C7 |
H10 |
1.100 |
1.089 |
| C7 |
H11 |
1.100 |
1.090 |
| N2 |
H12 |
1.000 |
0.970 |
| N2 |
H13 |
1.000 |
0.971 |
| O3' |
H14 |
0.950 |
0.967 |
| OP2 |
H16 |
0.950 |
0.968 |
| P |
OP3 |
1.588 |
1.610 |
| OP3 |
H15 |
0.950 |
0.967 |
Bond Angles for JSP
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H4 |
111.6 |
110.5 |
| O5' |
P |
OP2 |
107.6 |
109.4 |
| O5' |
P |
OP1 |
108.5 |
109.5 |
| O5' |
P |
OP3 |
102.9 |
109.5 |
| O5' |
C5' |
H6 |
108.7 |
109.5 |
| O5' |
C5' |
H7 |
108.7 |
109.4 |
| C3' |
C4' |
C5' |
116.6 |
109.9 |
| C3' |
C4' |
O4' |
105.8 |
107.4 |
| C4' |
C3' |
H4 |
110.1 |
110.5 |
| C3' |
C4' |
H5 |
107.5 |
109.9 |
| C3' |
C2' |
H2 |
111.8 |
110.9 |
| C3' |
C2' |
H3 |
111.8 |
110.9 |
| OP1 |
P |
OP2 |
119.5 |
109.5 |
| P |
OP2 |
H16 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
107.4 |
109.5 |
| OP1 |
P |
OP3 |
109.7 |
109.5 |
| C5' |
C4' |
O4' |
110.8 |
110.0 |
| C5' |
C4' |
H5 |
107.5 |
109.9 |
| C4' |
C5' |
H6 |
108.7 |
109.5 |
| C4' |
C5' |
H7 |
108.7 |
109.5 |
| O4' |
C4' |
H5 |
108.4 |
109.8 |
| C2' |
C1' |
H1 |
109.7 |
110.7 |
| O4' |
C1' |
H1 |
111.2 |
110.6 |
| C1' |
C1 |
C6 |
117.3 |
120.5 |
| C1' |
C1 |
C2 |
124.0 |
120.5 |
| C2 |
C1 |
C6 |
118.7 |
119.0 |
| C1 |
C6 |
N5 |
119.0 |
119.3 |
| C1 |
C6 |
H8 |
120.5 |
120.4 |
| C1 |
C2 |
N3 |
121.3 |
119.6 |
| C6 |
N5 |
C7 |
122.2 |
119.9 |
| N5 |
C6 |
H8 |
120.5 |
120.4 |
| N2 |
C2 |
N3 |
121.5 |
120.2 |
| C2 |
N3 |
C4 |
122.7 |
120.7 |
| N5 |
C7 |
H9 |
109.5 |
109.5 |
| N5 |
C7 |
H10 |
109.5 |
109.5 |
| N5 |
C7 |
H11 |
109.5 |
109.5 |
| N5 |
C4 |
O4 |
120.3 |
119.4 |
| N3 |
C4 |
O4 |
120.1 |
119.5 |
| H2 |
C2' |
H3 |
109.4 |
110.8 |
| H6 |
C5' |
H7 |
109.5 |
109.5 |
| H9 |
C7 |
H10 |
109.5 |
109.5 |
| H9 |
C7 |
H11 |
109.5 |
109.5 |
| H10 |
C7 |
H11 |
109.4 |
109.5 |
| H12 |
N2 |
H13 |
120.0 |
120.0 |
| P |
OP3 |
H15 |
109.5 |
114.0 |
Torsion Angles for JSP
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
C4' |
O4' |
260.1 |
239.3 |
| C4' |
C3' |
O3' |
H4 |
238.4 |
237.4 |
| O3' |
C3' |
C4' |
H5 |
15.8 |
358.7 |
| O3' |
C3' |
C2' |
H2 |
198.4 |
339.6 |
| O3' |
C3' |
C2' |
H3 |
321.5 |
216.1 |
| P |
O5' |
C5' |
H6 |
242.3 |
60.0 |
| P |
O5' |
C5' |
H7 |
1.4 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
229.4 |
240.0 |
| O5' |
P |
OP2 |
H16 |
235.8 |
60.0 |
| OP2 |
P |
O5' |
OP3 |
246.9 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
116.2 |
120.0 |
| O5' |
P |
OP3 |
H15 |
115.4 |
180.0 |
| O5' |
C5' |
C4' |
H5 |
109.8 |
306.0 |
| C4' |
C5' |
O5' |
H6 |
239.6 |
120.0 |
| C4' |
C5' |
O5' |
H7 |
120.4 |
240.0 |
| H6 |
C5' |
O5' |
H7 |
240.9 |
120.0 |
| O3' |
C3' |
C4' |
H4 |
122.5 |
122.6 |
| C4' |
C3' |
C2' |
H2 |
81.3 |
220.9 |
| C4' |
C3' |
C2' |
H3 |
204.4 |
97.4 |
| C5' |
C4' |
C3' |
O4' |
236.3 |
240.5 |
| C5' |
C4' |
C3' |
H5 |
120.7 |
121.0 |
| C3' |
C4' |
C5' |
H6 |
228.7 |
305.0 |
| C3' |
C4' |
C5' |
H7 |
109.6 |
65.0 |
| O4' |
C4' |
C3' |
H5 |
244.3 |
240.6 |
| C3' |
C2' |
C1' |
H1 |
282.9 |
278.3 |
| H2 |
C2' |
C3' |
H3 |
236.9 |
123.5 |
| O5' |
P |
OP2 |
OP1 |
235.8 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
110.1 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
234.3 |
240.0 |
| OP2 |
P |
OP3 |
H15 |
228.7 |
300.0 |
| O5' |
P |
OP1 |
OP2 |
123.7 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
248.3 |
240.0 |
| OP1 |
P |
OP2 |
H16 |
0.0 |
180.0 |
| OP2 |
P |
OP1 |
OP3 |
124.6 |
120.0 |
| OP1 |
P |
OP3 |
H15 |
360.0 |
60.0 |
| O5' |
C5' |
C4' |
H6 |
120.4 |
240.0 |
| O5' |
C5' |
C4' |
H7 |
239.6 |
119.9 |
| C3' |
C4' |
C5' |
O4' |
121.1 |
117.9 |
| C5' |
C4' |
C3' |
H4 |
14.0 |
357.1 |
| C3' |
C4' |
C5' |
H5 |
239.3 |
239.0 |
| O4' |
C4' |
C5' |
H5 |
118.3 |
121.0 |
| H6 |
C5' |
C4' |
H7 |
119.1 |
240.0 |
| C3' |
C4' |
O4' |
C5' |
232.7 |
240.5 |
| O4' |
C4' |
C3' |
H4 |
137.6 |
116.7 |
| C3' |
C4' |
O4' |
H5 |
115.0 |
119.5 |
| C5' |
C4' |
O4' |
H5 |
242.3 |
238.9 |
| O4' |
C4' |
C5' |
H6 |
107.7 |
187.0 |
| O4' |
C4' |
C5' |
H7 |
348.5 |
307.0 |
| C4' |
O4' |
C1' |
H1 |
87.5 |
78.8 |
| O4' |
C1' |
C2' |
H1 |
119.3 |
118.6 |
| C2' |
C1' |
C1 |
C6 |
333.3 |
117.2 |
| C2' |
C1' |
O4' |
H1 |
241.7 |
241.4 |
| C2 |
C1 |
C1' |
C6 |
179.8 |
180.3 |
| C1' |
C1 |
C6 |
N5 |
180.0 |
180.3 |
| C1' |
C1 |
C6 |
H8 |
360.0 |
0.2 |
| C1' |
C1 |
C2 |
N3 |
180.0 |
179.7 |
| C1' |
C1 |
C6 |
C2 |
179.8 |
180.3 |
| C6 |
C1 |
C2 |
N3 |
359.8 |
360.0 |
| C1 |
C6 |
N5 |
C7 |
179.9 |
180.0 |
| N5 |
C6 |
C1 |
H8 |
180.0 |
180.1 |
| C1' |
C1 |
C2 |
C6 |
180.2 |
179.7 |
| C2 |
C1 |
C6 |
N5 |
0.2 |
0.0 |
| C2 |
C1 |
C6 |
H8 |
180.2 |
179.9 |
| N2 |
C2 |
C1 |
N3 |
180.1 |
180.0 |
| C1 |
C2 |
N3 |
C4 |
0.1 |
0.0 |
| C1 |
C6 |
N5 |
H8 |
180.0 |
179.9 |
| C6 |
N5 |
C7 |
H9 |
180.0 |
89.9 |
| C6 |
N5 |
C7 |
H10 |
300.0 |
210.0 |
| C6 |
N5 |
C7 |
H11 |
60.0 |
330.0 |
| C6 |
N5 |
C4 |
O4 |
180.1 |
180.0 |
| C1 |
C2 |
N2 |
N3 |
179.9 |
180.0 |
| N2 |
C2 |
N3 |
C4 |
180.0 |
180.0 |
| N3 |
C2 |
C1 |
C6 |
359.8 |
360.0 |
| C2 |
N3 |
C4 |
O4 |
179.9 |
180.1 |
| C7 |
N5 |
C6 |
H8 |
359.9 |
0.1 |
| C7 |
N5 |
C4 |
O4 |
0.1 |
359.9 |
| H9 |
C7 |
N5 |
H10 |
240.0 |
239.9 |
| H9 |
C7 |
N5 |
H11 |
120.0 |
120.0 |
| H10 |
C7 |
N5 |
H11 |
240.0 |
240.0 |
| C1 |
C6 |
N5 |
C4 |
359.9 |
359.9 |
| N3 |
C4 |
N5 |
O4 |
179.9 |
180.1 |
| N5 |
C4 |
N3 |
O4 |
180.1 |
179.9 |
| H1 |
C1' |
C1 |
C6 |
211.1 |
354.3 |
| H1 |
C1' |
C1 |
C2 |
30.8 |
174.6 |
| C3' |
C2' |
H2 |
H3 |
124.4 |
236.4 |
| H2 |
C2' |
C1' |
H1 |
164.5 |
36.6 |
| C3' |
C2' |
H3 |
H2 |
235.6 |
123.6 |
| H3 |
C2' |
C1' |
H1 |
41.4 |
160.1 |
| H4 |
C3' |
C4' |
C5' |
14.0 |
357.1 |
| H4 |
C3' |
C4' |
O4' |
137.6 |
116.7 |
| H4 |
C3' |
C4' |
H5 |
253.3 |
236.1 |
| H4 |
C3' |
C2' |
H2 |
324.1 |
102.2 |
| H4 |
C3' |
C2' |
H3 |
87.2 |
338.7 |
| C3' |
C4' |
H5 |
C5' |
126.3 |
121.0 |
| C3' |
C4' |
H5 |
O4' |
246.1 |
242.1 |
| H5 |
C4' |
C3' |
H4 |
253.3 |
236.1 |
| C5' |
C4' |
H5 |
O4' |
119.8 |
121.1 |
| H5 |
C4' |
C5' |
H6 |
349.4 |
66.0 |
| H5 |
C4' |
C5' |
H7 |
230.3 |
186.0 |
| O5' |
C5' |
H6 |
H7 |
118.6 |
240.0 |
| H6 |
C5' |
C4' |
O4' |
107.7 |
187.0 |
| H6 |
C5' |
C4' |
H5 |
349.4 |
66.0 |
| C4' |
C5' |
H6 |
H7 |
241.3 |
120.0 |
| O5' |
C5' |
H7 |
H6 |
241.4 |
120.0 |
| H7 |
C5' |
C4' |
O4' |
348.5 |
307.0 |
| H7 |
C5' |
C4' |
H5 |
230.3 |
186.0 |
| C4' |
C5' |
H7 |
H6 |
118.7 |
240.0 |
| C1 |
C6 |
H8 |
N5 |
180.0 |
180.1 |
| H8 |
C6 |
N5 |
C7 |
359.9 |
0.1 |
| N5 |
C7 |
H9 |
H10 |
120.0 |
120.0 |
| N5 |
C7 |
H9 |
H11 |
240.0 |
240.0 |
| H10 |
C7 |
H9 |
H11 |
120.0 |
120.0 |
| N5 |
C7 |
H10 |
H9 |
240.0 |
240.0 |
| N5 |
C7 |
H10 |
H11 |
120.0 |
120.0 |
| H9 |
C7 |
H10 |
H11 |
240.0 |
240.0 |
| N5 |
C7 |
H11 |
H9 |
120.0 |
120.0 |
| N5 |
C7 |
H11 |
H10 |
240.0 |
240.0 |
| H9 |
C7 |
H11 |
H10 |
120.0 |
120.0 |
| H12 |
N2 |
C2 |
N3 |
360.0 |
180.0 |
| H13 |
N2 |
C2 |
N3 |
180.0 |
0.0 |
| H14 |
O3' |
C3' |
H4 |
301.6 |
302.6 |
| H16 |
OP2 |
P |
OP3 |
125.7 |
300.0 |
| O5' |
P |
OP3 |
OP2 |
246.7 |
240.0 |
| O5' |
P |
OP3 |
OP1 |
115.4 |
120.0 |
| OP1 |
P |
OP3 |
OP2 |
131.3 |
120.0 |
| OP3 |
P |
OP2 |
H16 |
125.7 |
300.0 |