PDB Chemical Component JKM
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 JKM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O20 |
P |
1.704 |
1.649 |
| O3P |
P |
1.495 |
1.480 |
| P |
O2P |
1.606 |
1.610 |
| P |
O2' |
1.736 |
1.644 |
| C1' |
N1 |
1.520 |
1.466 |
| C2 |
N1 |
1.501 |
1.345 |
| N1 |
C6 |
1.418 |
1.368 |
| O2 |
C2 |
1.203 |
1.215 |
| C2 |
N3 |
1.418 |
1.346 |
| N3 |
C4 |
1.355 |
1.349 |
| C4 |
C5 |
1.435 |
1.416 |
| C4 |
O4 |
1.338 |
1.218 |
| C6 |
C5 |
1.359 |
1.350 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.081 |
1.080 |
| O4' |
C1' |
1.451 |
1.456 |
| C2' |
C1' |
1.535 |
1.515 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
C2' |
1.583 |
1.572 |
| C2' |
O2' |
1.383 |
1.406 |
| C2' |
H2' |
1.100 |
1.090 |
| O20 |
C3' |
1.395 |
1.414 |
| O2P |
HO2P |
0.950 |
0.967 |
| C4' |
C3' |
1.537 |
1.510 |
| C3' |
H3' |
1.100 |
1.090 |
| C4' |
C5' |
1.553 |
1.530 |
| C4' |
O4' |
1.433 |
1.452 |
| C4' |
H4' |
1.099 |
1.090 |
| O5' |
C5' |
1.408 |
1.428 |
| C5' |
H5' |
1.101 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
HO5' |
0.950 |
0.967 |
| N3 |
HN3 |
1.000 |
0.970 |
Bond Angles for JKM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O20 |
P |
O2P |
104.1 |
110.7 |
| O2' |
P |
O2P |
106.4 |
110.7 |
| P |
O2P |
HO2P |
109.5 |
113.9 |
| P |
O2' |
C2' |
105.5 |
101.8 |
| C2 |
N1 |
C6 |
118.0 |
120.6 |
| N1 |
C6 |
C5 |
123.5 |
119.7 |
| N1 |
C6 |
H6 |
118.3 |
120.2 |
| O2 |
C2 |
N3 |
120.3 |
119.5 |
| C2 |
N3 |
C4 |
119.2 |
120.2 |
| C2 |
N3 |
HN3 |
120.4 |
119.9 |
| N3 |
C4 |
C5 |
125.4 |
119.4 |
| N3 |
C4 |
O4 |
121.7 |
120.3 |
| C4 |
N3 |
HN3 |
120.4 |
119.9 |
| O4 |
C4 |
C5 |
112.9 |
120.3 |
| C4 |
C5 |
H5 |
121.8 |
120.4 |
| C6 |
C5 |
H5 |
121.9 |
120.5 |
| O4' |
C1' |
H1' |
105.5 |
110.9 |
| C2' |
C1' |
H1' |
104.7 |
110.7 |
| C3' |
C2' |
H2' |
109.2 |
108.6 |
| O2' |
C2' |
H2' |
112.1 |
109.7 |
| O20 |
C3' |
H3' |
108.6 |
110.0 |
| C4' |
C3' |
H3' |
106.9 |
109.2 |
| O4' |
C4' |
C5' |
111.6 |
110.2 |
| C5' |
C4' |
H4' |
111.2 |
110.2 |
| C4' |
C5' |
H5' |
109.6 |
109.4 |
| C4' |
C5' |
H5'A |
109.6 |
109.5 |
| O4' |
C4' |
H4' |
113.1 |
110.2 |
| O5' |
C5' |
H5' |
109.6 |
109.5 |
| O5' |
C5' |
H5'A |
109.6 |
109.5 |
| H5' |
C5' |
H5'A |
109.4 |
109.5 |
Torsion Angles for JKM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2' |
P |
O20 |
O2P |
252.8 |
241.6 |
| O20 |
P |
O2P |
HO2P |
133.2 |
66.3 |
| O3P |
P |
O2P |
HO2P |
360.0 |
303.1 |
| O2P |
P |
O2' |
C2' |
221.4 |
232.4 |
| O20 |
P |
O2' |
O2P |
105.0 |
118.4 |
| O2' |
P |
O2P |
HO2P |
228.4 |
180.0 |
| P |
O2' |
C2' |
H2' |
298.8 |
280.5 |
| C1' |
N1 |
C6 |
H6 |
359.8 |
0.2 |
| C2 |
N1 |
C6 |
C5 |
359.1 |
0.0 |
| C2 |
N1 |
C6 |
H6 |
179.1 |
180.0 |
| N1 |
C6 |
C5 |
H5 |
182.0 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
179.7 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.8 |
180.0 |
| O2 |
C2 |
N3 |
HN3 |
0.7 |
359.9 |
| N3 |
C2 |
N1 |
C6 |
359.2 |
359.9 |
| C2 |
N3 |
C4 |
C5 |
360.0 |
359.9 |
| C2 |
N3 |
C4 |
O4 |
179.8 |
180.0 |
| C4 |
N3 |
C2 |
HN3 |
180.0 |
180.1 |
| C2 |
N3 |
C4 |
HN3 |
180.0 |
179.9 |
| O4 |
C4 |
N3 |
C5 |
179.8 |
180.1 |
| N3 |
C4 |
C5 |
H5 |
178.4 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
2.0 |
0.0 |
| N3 |
C4 |
C5 |
O4 |
179.8 |
180.1 |
| C5 |
C4 |
N3 |
HN3 |
180.0 |
180.1 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.9 |
| N3 |
C4 |
O4 |
C5 |
180.2 |
179.9 |
| O4 |
C4 |
N3 |
HN3 |
359.8 |
0.1 |
| O4 |
C4 |
C5 |
H5 |
358.6 |
0.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.0 |
| H6 |
C6 |
C5 |
H5 |
2.0 |
360.0 |
| C2' |
C1' |
O4' |
H1' |
109.5 |
118.6 |
| P |
O2' |
C2' |
C1' |
158.4 |
148.0 |
| O4' |
C1' |
C2' |
H1' |
249.8 |
241.3 |
| C3' |
C2' |
C1' |
H1' |
65.0 |
75.7 |
| O2' |
C2' |
C3' |
H2' |
242.8 |
243.3 |
| C2' |
O2' |
P |
O2P |
221.4 |
232.4 |
| O2' |
C2' |
C1' |
H1' |
319.1 |
321.8 |
| C3' |
C2' |
O2' |
H2' |
114.9 |
116.0 |
| H2' |
C2' |
C1' |
H1' |
178.0 |
189.2 |
| C3' |
O20 |
P |
O2P |
105.0 |
93.9 |
| O20 |
C3' |
C2' |
H2' |
62.1 |
59.3 |
| C4' |
C3' |
O20 |
H3' |
230.5 |
228.2 |
| C4' |
C3' |
C2' |
H2' |
288.6 |
291.0 |
| O20 |
C3' |
C4' |
H3' |
130.2 |
132.1 |
| H3' |
C3' |
C2' |
H2' |
176.2 |
176.1 |
| C5' |
C4' |
C3' |
H3' |
330.4 |
324.7 |
| O4' |
C4' |
C5' |
H4' |
127.3 |
121.9 |
| O5' |
C5' |
C4' |
H5' |
240.1 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H5'A |
239.9 |
240.0 |
| C4' |
O4' |
C1' |
H1' |
284.3 |
266.3 |
| O4' |
C4' |
C3' |
H3' |
87.8 |
83.7 |
| C5' |
C4' |
O4' |
H4' |
233.7 |
238.2 |
| O4' |
C4' |
C5' |
H5' |
292.8 |
188.7 |
| O4' |
C4' |
C5' |
H5'A |
52.9 |
308.7 |
| H4' |
C4' |
C3' |
H3' |
209.9 |
202.9 |
| O4' |
C4' |
H4' |
C5' |
233.5 |
238.2 |
| H4' |
C4' |
C5' |
H5' |
165.5 |
66.9 |
| H4' |
C4' |
C5' |
H5'A |
285.6 |
186.8 |
| O5' |
C5' |
C4' |
H4' |
45.5 |
306.8 |
| C4' |
C5' |
O5' |
H5' |
119.9 |
120.0 |
| C4' |
C5' |
O5' |
H5'A |
240.0 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.1 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
165.5 |
66.9 |
| C4' |
C5' |
H5' |
H5'A |
120.2 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
239.8 |
240.0 |
| H5'A |
C5' |
C4' |
H4' |
285.6 |
186.8 |
| C4' |
C5' |
H5'A |
H5' |
239.8 |
240.1 |
| O5' |
C5' |
H5'A |
H5' |
120.1 |
120.0 |
| HO5' |
O5' |
C5' |
H5' |
60.1 |
60.0 |
| HO5' |
O5' |
C5' |
H5'A |
300.0 |
300.0 |
| C2 |
N3 |
HN3 |
C4 |
180.0 |
180.1 |
| HN3 |
N3 |
C4 |
C5 |
180.0 |
180.1 |
| HN3 |
N3 |
C4 |
O4 |
359.8 |
0.1 |