PDB Chemical Component 2ST
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 2ST
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
1.611 |
|
OP3 |
HOP3 |
0.950 |
|
P |
OP1 |
1.468 |
|
P |
OP2 |
1.491 |
|
P |
O5' |
1.592 |
|
OP2 |
HOP2 |
0.950 |
|
O5' |
C5' |
1.414 |
|
N1 |
C6 |
1.389 |
|
N1 |
C2 |
1.389 |
|
N1 |
C1' |
1.500 |
|
C6 |
C5 |
1.400 |
|
C6 |
H6 |
1.080 |
|
C2 |
O2 |
1.220 |
|
C2 |
N3 |
1.372 |
|
N3 |
C4 |
1.386 |
|
N3 |
HN3 |
1.001 |
|
C4 |
O4 |
1.222 |
|
C4 |
C5 |
1.500 |
|
C5 |
C5A |
1.504 |
|
C5A |
H5A1 |
1.100 |
|
C5A |
H5A2 |
1.100 |
|
C5A |
H5A3 |
1.100 |
|
C2' |
C1' |
1.502 |
|
C2' |
C3' |
1.519 |
|
C2' |
SE |
2.058 |
|
C2' |
H2' |
1.100 |
|
C5' |
C4' |
1.506 |
|
C5' |
H5' |
1.100 |
|
C5' |
H5'' |
1.100 |
|
C4' |
O4' |
1.444 |
|
C4' |
C3' |
1.514 |
|
C4' |
H4' |
1.100 |
|
O4' |
C1' |
1.444 |
|
C1' |
H1' |
1.100 |
|
C3' |
O3' |
1.368 |
|
C3' |
H3' |
1.100 |
|
SE |
CA' |
1.960 |
|
CA' |
HA'1 |
1.100 |
|
CA' |
HA'2 |
1.101 |
|
CA' |
HA'3 |
1.100 |
|
O3' |
HO3' |
0.950 |
|
Bond Angles for 2ST
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
104.3 |
|
OP3 |
P |
OP1 |
104.3 |
|
OP3 |
P |
OP2 |
110.9 |
|
OP3 |
P |
O5' |
104.8 |
|
OP1 |
P |
OP2 |
121.1 |
|
OP1 |
P |
O5' |
107.3 |
|
OP2 |
P |
O5' |
107.3 |
|
P |
OP2 |
HOP2 |
110.9 |
|
P |
O5' |
C5' |
119.9 |
|
O5' |
C5' |
C4' |
110.3 |
|
O5' |
C5' |
H5' |
109.2 |
|
O5' |
C5' |
H5'' |
109.0 |
|
C6 |
N1 |
C2 |
121.0 |
|
C6 |
N1 |
C1' |
124.2 |
|
N1 |
C6 |
C5 |
122.7 |
|
N1 |
C6 |
H6 |
118.6 |
|
C2 |
N1 |
C1' |
114.8 |
|
N1 |
C2 |
O2 |
121.9 |
|
N1 |
C2 |
N3 |
116.7 |
|
N1 |
C1' |
C2' |
107.2 |
|
N1 |
C1' |
O4' |
103.0 |
|
N1 |
C1' |
H1' |
114.3 |
|
C5 |
C6 |
H6 |
118.6 |
|
C6 |
C5 |
C4 |
117.3 |
|
C6 |
C5 |
C5A |
123.8 |
|
O2 |
C2 |
N3 |
121.4 |
|
C2 |
N3 |
C4 |
127.6 |
|
C2 |
N3 |
HN3 |
116.2 |
|
C4 |
N3 |
HN3 |
116.2 |
|
N3 |
C4 |
O4 |
120.0 |
|
N3 |
C4 |
C5 |
114.7 |
|
O4 |
C4 |
C5 |
125.3 |
|
C4 |
C5 |
C5A |
118.9 |
|
C5 |
C5A |
H5A1 |
109.5 |
|
C5 |
C5A |
H5A2 |
109.4 |
|
C5 |
C5A |
H5A3 |
109.4 |
|
H5A1 |
C5A |
H5A2 |
109.5 |
|
H5A1 |
C5A |
H5A3 |
109.5 |
|
H5A2 |
C5A |
H5A3 |
109.5 |
|
C1' |
C2' |
C3' |
101.1 |
|
C1' |
C2' |
SE |
104.5 |
|
C1' |
C2' |
H2' |
118.2 |
|
C2' |
C1' |
O4' |
107.1 |
|
C2' |
C1' |
H1' |
110.5 |
|
C3' |
C2' |
SE |
111.3 |
|
C3' |
C2' |
H2' |
112.2 |
|
C2' |
C3' |
C4' |
101.8 |
|
C2' |
C3' |
O3' |
108.9 |
|
C2' |
C3' |
H3' |
116.2 |
|
SE |
C2' |
H2' |
109.1 |
|
C2' |
SE |
CA' |
99.6 |
|
C4' |
C5' |
H5' |
109.2 |
|
C4' |
C5' |
H5'' |
109.0 |
|
C5' |
C4' |
O4' |
107.4 |
|
C5' |
C4' |
C3' |
117.1 |
|
C5' |
C4' |
H4' |
103.6 |
|
H5' |
C5' |
H5'' |
110.1 |
|
O4' |
C4' |
C3' |
101.5 |
|
O4' |
C4' |
H4' |
118.7 |
|
C4' |
O4' |
C1' |
108.7 |
|
C3' |
C4' |
H4' |
109.2 |
|
C4' |
C3' |
O3' |
113.7 |
|
C4' |
C3' |
H3' |
111.6 |
|
O4' |
C1' |
H1' |
114.2 |
|
O3' |
C3' |
H3' |
104.9 |
|
C3' |
O3' |
HO3' |
109.5 |
|
SE |
CA' |
HA'1 |
109.5 |
|
SE |
CA' |
HA'2 |
109.5 |
|
SE |
CA' |
HA'3 |
109.4 |
|
HA'1 |
CA' |
HA'2 |
109.5 |
|
HA'1 |
CA' |
HA'3 |
109.4 |
|
HA'2 |
CA' |
HA'3 |
109.5 |
|
Torsion Angles for 2ST
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
131.9 |
|
OP1 |
P |
OP3 |
O5' |
247.4 |
|
OP2 |
P |
OP3 |
O5' |
115.5 |
|
OP3 |
P |
OP2 |
HOP2 |
180.0 |
|
OP3 |
P |
O5' |
C5' |
294.8 |
|
HOP3 |
OP3 |
P |
OP1 |
180.0 |
|
HOP3 |
OP3 |
P |
OP2 |
48.1 |
|
HOP3 |
OP3 |
P |
O5' |
292.7 |
|
OP1 |
P |
OP3 |
HOP3 |
180.0 |
|
OP3 |
P |
OP1 |
OP2 |
234.3 |
|
OP3 |
P |
OP1 |
O5' |
110.9 |
|
OP2 |
P |
OP1 |
O5' |
236.6 |
|
OP1 |
P |
OP2 |
HOP2 |
57.4 |
|
OP1 |
P |
O5' |
C5' |
45.3 |
|
OP2 |
P |
OP3 |
HOP3 |
48.1 |
|
OP3 |
P |
OP2 |
OP1 |
122.6 |
|
OP3 |
P |
OP2 |
O5' |
246.0 |
|
OP1 |
P |
OP2 |
O5' |
123.4 |
|
OP2 |
P |
O5' |
C5' |
176.8 |
|
O5' |
P |
OP3 |
HOP3 |
292.7 |
|
OP3 |
P |
O5' |
OP1 |
249.5 |
|
OP3 |
P |
O5' |
OP2 |
118.0 |
|
OP1 |
P |
O5' |
OP2 |
228.5 |
|
O5' |
P |
OP2 |
HOP2 |
294.0 |
|
P |
O5' |
C5' |
C4' |
174.6 |
|
P |
O5' |
C5' |
H5' |
54.6 |
|
P |
O5' |
C5' |
H5'' |
294.3 |
|
HOP2 |
OP2 |
P |
O5' |
294.0 |
|
C4' |
C5' |
O5' |
H5' |
120.0 |
|
C4' |
C5' |
O5' |
H5'' |
240.4 |
|
O5' |
C5' |
C4' |
O4' |
294.0 |
|
O5' |
C5' |
C4' |
C3' |
47.3 |
|
O5' |
C5' |
C4' |
H4' |
167.6 |
|
H5' |
C5' |
O5' |
H5'' |
120.4 |
|
C2 |
N1 |
C6 |
C1' |
180.8 |
|
C6 |
N1 |
C2 |
O2 |
176.0 |
|
C6 |
N1 |
C2 |
N3 |
357.4 |
|
C6 |
N1 |
C1' |
C2' |
267.3 |
|
C6 |
N1 |
C1' |
O4' |
20.1 |
|
C6 |
N1 |
C1' |
H1' |
144.6 |
|
C5 |
C6 |
N1 |
H6 |
180.0 |
|
N1 |
C6 |
C5 |
C4 |
0.7 |
|
N1 |
C6 |
C5 |
C5A |
180.3 |
|
C6 |
N1 |
C2 |
C1' |
179.3 |
|
C2 |
N1 |
C6 |
C5 |
1.4 |
|
C2 |
N1 |
C6 |
H6 |
181.4 |
|
C2 |
N1 |
C1' |
C2' |
86.6 |
|
C2 |
N1 |
C1' |
O4' |
199.4 |
|
C2 |
N1 |
C1' |
H1' |
323.8 |
|
O2 |
C2 |
N1 |
N3 |
178.5 |
|
N1 |
C2 |
N3 |
C4 |
1.7 |
|
N1 |
C2 |
N3 |
HN3 |
181.7 |
|
C6 |
N1 |
C1' |
C2 |
180.8 |
|
C1' |
N1 |
C6 |
C5 |
180.6 |
|
C1' |
N1 |
C6 |
H6 |
0.6 |
|
C1' |
N1 |
C2 |
O2 |
356.7 |
|
C1' |
N1 |
C2 |
N3 |
178.2 |
|
N1 |
C1' |
C2' |
C3' |
87.5 |
|
N1 |
C1' |
C2' |
SE |
203.2 |
|
N1 |
C1' |
C2' |
H2' |
324.7 |
|
C2' |
C1' |
N1 |
O4' |
247.2 |
|
C2' |
C1' |
N1 |
H1' |
122.8 |
|
C4' |
O4' |
C1' |
N1 |
242.4 |
|
O4' |
C1' |
N1 |
H1' |
235.6 |
|
C5 |
C6 |
N1 |
C2 |
1.4 |
|
C5 |
C6 |
N1 |
C1' |
180.6 |
|
N1 |
C6 |
C5 |
H6 |
180.0 |
|
N3 |
C4 |
C5 |
C6 |
358.5 |
|
O4 |
C4 |
C5 |
C6 |
177.9 |
|
C4 |
C5 |
C6 |
C5A |
180.4 |
|
C6 |
C5 |
C5A |
H5A1 |
60.1 |
|
C6 |
C5 |
C5A |
H5A2 |
180.2 |
|
C6 |
C5 |
C5A |
H5A3 |
300.1 |
|
H6 |
C6 |
N1 |
C2 |
181.4 |
|
H6 |
C6 |
N1 |
C1' |
0.6 |
|
N1 |
C6 |
H6 |
C5 |
180.0 |
|
H6 |
C6 |
C5 |
C4 |
180.7 |
|
H6 |
C6 |
C5 |
C5A |
0.3 |
|
O2 |
C2 |
N1 |
C1' |
356.7 |
|
N1 |
C2 |
O2 |
N3 |
181.5 |
|
O2 |
C2 |
N3 |
C4 |
183.1 |
|
O2 |
C2 |
N3 |
HN3 |
3.1 |
|
N3 |
C2 |
N1 |
C1' |
178.2 |
|
N1 |
C2 |
N3 |
O2 |
178.5 |
|
C4 |
N3 |
C2 |
HN3 |
180.0 |
|
C2 |
N3 |
C4 |
O4 |
180.9 |
|
C2 |
N3 |
C4 |
C5 |
0.4 |
|
C6 |
C5 |
C4 |
N3 |
358.5 |
|
C2 |
N3 |
C4 |
HN3 |
180.0 |
|
O4 |
C4 |
N3 |
C5 |
180.5 |
|
N3 |
C4 |
C5 |
C5A |
178.9 |
|
C2 |
N3 |
HN3 |
C4 |
180.0 |
|
HN3 |
N3 |
C4 |
O4 |
0.8 |
|
HN3 |
N3 |
C4 |
C5 |
180.4 |
|
C6 |
C5 |
C4 |
O4 |
177.9 |
|
O4 |
C4 |
N3 |
HN3 |
0.8 |
|
N3 |
C4 |
O4 |
C5 |
179.5 |
|
O4 |
C4 |
C5 |
C5A |
358.4 |
|
C4 |
C5 |
C6 |
H6 |
180.7 |
|
C6 |
C5 |
C4 |
C5A |
179.6 |
|
C5 |
C4 |
N3 |
HN3 |
180.4 |
|
N3 |
C4 |
C5 |
O4 |
180.5 |
|
C4 |
C5 |
C5A |
H5A1 |
239.7 |
|
C4 |
C5 |
C5A |
H5A2 |
359.7 |
|
C4 |
C5 |
C5A |
H5A3 |
119.7 |
|
C5A |
C5 |
C6 |
H6 |
0.3 |
|
C6 |
C5 |
C5A |
C4 |
180.4 |
|
H5A1 |
C5A |
C5 |
H5A2 |
240.0 |
|
H5A1 |
C5A |
C5 |
H5A3 |
120.0 |
|
H5A2 |
C5A |
C5 |
H5A3 |
240.0 |
|
C5 |
C5A |
H5A1 |
H5A2 |
120.0 |
|
C5 |
C5A |
H5A1 |
H5A3 |
240.0 |
|
H5A2 |
C5A |
H5A1 |
H5A3 |
120.0 |
|
C5 |
C5A |
H5A2 |
H5A1 |
240.0 |
|
C5 |
C5A |
H5A2 |
H5A3 |
119.9 |
|
H5A1 |
C5A |
H5A2 |
H5A3 |
240.0 |
|
C5 |
C5A |
H5A3 |
H5A1 |
120.0 |
|
C5 |
C5A |
H5A3 |
H5A2 |
240.0 |
|
H5A1 |
C5A |
H5A3 |
H5A2 |
120.0 |
|
N1 |
C1' |
C2' |
O4' |
109.9 |
|
N1 |
C1' |
C2' |
H1' |
234.9 |
|
C3' |
C2' |
C1' |
SE |
244.3 |
|
C3' |
C2' |
C1' |
H2' |
122.8 |
|
C1' |
C2' |
C3' |
C4' |
40.0 |
|
C1' |
C2' |
C3' |
O3' |
160.4 |
|
C1' |
C2' |
C3' |
H3' |
278.5 |
|
SE |
C2' |
C1' |
H2' |
238.5 |
|
C1' |
C2' |
SE |
CA' |
82.5 |
|
C4' |
O4' |
C1' |
C2' |
355.2 |
|
O4' |
C1' |
C2' |
H1' |
125.0 |
|
C1' |
C2' |
C3' |
SE |
110.5 |
|
C1' |
C2' |
C3' |
H2' |
233.1 |
|
C3' |
C2' |
C1' |
O4' |
337.6 |
|
C3' |
C2' |
C1' |
H1' |
212.6 |
|
SE |
C2' |
C3' |
H2' |
122.6 |
|
C3' |
C2' |
SE |
CA' |
190.8 |
|
C5' |
C4' |
C3' |
C2' |
200.1 |
|
O4' |
C4' |
C3' |
C2' |
316.6 |
|
C2' |
C3' |
C4' |
H4' |
82.8 |
|
C4' |
C3' |
C2' |
O3' |
239.6 |
|
C4' |
C3' |
C2' |
H3' |
121.5 |
|
O3' |
C3' |
C2' |
H3' |
241.9 |
|
C2' |
C3' |
O3' |
HO3' |
344.9 |
|
C1' |
C2' |
SE |
C3' |
251.7 |
|
C1' |
C2' |
SE |
H2' |
127.3 |
|
SE |
C2' |
C1' |
O4' |
93.3 |
|
SE |
C2' |
C1' |
H1' |
328.3 |
|
C3' |
C2' |
SE |
H2' |
235.7 |
|
SE |
C2' |
C3' |
C4' |
289.5 |
|
SE |
C2' |
C3' |
O3' |
49.9 |
|
SE |
C2' |
C3' |
H3' |
168.0 |
|
C2' |
SE |
CA' |
HA'1 |
305.7 |
|
C2' |
SE |
CA' |
HA'2 |
65.7 |
|
C2' |
SE |
CA' |
HA'3 |
185.8 |
|
C1' |
C2' |
H2' |
C3' |
117.0 |
|
C1' |
C2' |
H2' |
SE |
240.9 |
|
H2' |
C2' |
C1' |
O4' |
214.8 |
|
H2' |
C2' |
C1' |
H1' |
89.8 |
|
C3' |
C2' |
H2' |
SE |
123.8 |
|
H2' |
C2' |
C3' |
C4' |
166.9 |
|
H2' |
C2' |
C3' |
O3' |
287.3 |
|
H2' |
C2' |
C3' |
H3' |
45.4 |
|
H2' |
C2' |
SE |
CA' |
315.1 |
|
O5' |
C5' |
C4' |
H5' |
240.0 |
|
O5' |
C5' |
C4' |
H5'' |
119.6 |
|
C2' |
C3' |
C4' |
C5' |
200.1 |
|
H5' |
C5' |
C4' |
H5'' |
239.6 |
|
O4' |
C4' |
C5' |
C3' |
246.7 |
|
O4' |
C4' |
C5' |
H4' |
126.4 |
|
C5' |
C4' |
O4' |
C1' |
153.5 |
|
C3' |
C4' |
C5' |
H4' |
239.7 |
|
C5' |
C4' |
C3' |
O3' |
83.2 |
|
C5' |
C4' |
C3' |
H3' |
324.8 |
|
O5' |
C5' |
H5' |
C4' |
120.7 |
|
O5' |
C5' |
H5' |
H5'' |
240.4 |
|
C4' |
C5' |
H5' |
H5'' |
119.7 |
|
H5' |
C5' |
C4' |
O4' |
54.0 |
|
H5' |
C5' |
C4' |
C3' |
167.3 |
|
H5' |
C5' |
C4' |
H4' |
287.6 |
|
O5' |
C5' |
H5'' |
C4' |
239.6 |
|
O5' |
C5' |
H5'' |
H5' |
119.8 |
|
C4' |
C5' |
H5'' |
H5' |
240.2 |
|
H5'' |
C5' |
C4' |
O4' |
174.3 |
|
H5'' |
C5' |
C4' |
C3' |
287.6 |
|
H5'' |
C5' |
C4' |
H4' |
47.9 |
|
N1 |
C1' |
O4' |
C4' |
242.4 |
|
C2' |
C1' |
O4' |
C4' |
355.2 |
|
C2' |
C3' |
C4' |
O4' |
316.6 |
|
O4' |
C4' |
C5' |
H5' |
54.0 |
|
O4' |
C4' |
C5' |
H5'' |
174.3 |
|
C5' |
C4' |
O4' |
C3' |
123.4 |
|
C5' |
C4' |
O4' |
H4' |
243.1 |
|
C3' |
C4' |
O4' |
H4' |
119.7 |
|
O4' |
C4' |
C3' |
O3' |
199.7 |
|
O4' |
C4' |
C3' |
H3' |
81.3 |
|
C4' |
O4' |
C1' |
H1' |
118.0 |
|
C4' |
C3' |
C2' |
SE |
289.5 |
|
C4' |
C3' |
C2' |
H2' |
166.9 |
|
C2' |
C3' |
C4' |
O3' |
116.9 |
|
C2' |
C3' |
C4' |
H3' |
235.3 |
|
C3' |
C4' |
C5' |
H5' |
167.3 |
|
C3' |
C4' |
C5' |
H5'' |
287.6 |
|
C5' |
C4' |
C3' |
O4' |
243.5 |
|
C5' |
C4' |
C3' |
H4' |
117.3 |
|
O4' |
C4' |
C3' |
H4' |
233.8 |
|
C3' |
C4' |
O4' |
C1' |
30.0 |
|
O3' |
C3' |
C4' |
H3' |
118.4 |
|
C4' |
C3' |
O3' |
HO3' |
97.6 |
|
H4' |
C4' |
C5' |
H5' |
287.6 |
|
H4' |
C4' |
C5' |
H5'' |
47.9 |
|
C5' |
C4' |
H4' |
O4' |
118.9 |
|
C5' |
C4' |
H4' |
C3' |
234.5 |
|
O4' |
C4' |
H4' |
C3' |
115.6 |
|
H4' |
C4' |
O4' |
C1' |
270.4 |
|
H4' |
C4' |
C3' |
O3' |
325.9 |
|
H4' |
C4' |
C3' |
H3' |
207.5 |
|
N1 |
C1' |
O4' |
C2' |
247.2 |
|
N1 |
C1' |
O4' |
H1' |
124.5 |
|
O4' |
C1' |
C2' |
C3' |
337.6 |
|
O4' |
C1' |
C2' |
SE |
93.3 |
|
O4' |
C1' |
C2' |
H2' |
214.8 |
|
C2' |
C1' |
O4' |
H1' |
237.3 |
|
C1' |
O4' |
C4' |
C3' |
30.0 |
|
C1' |
O4' |
C4' |
H4' |
270.4 |
|
N1 |
C1' |
H1' |
C2' |
120.9 |
|
N1 |
C1' |
H1' |
O4' |
241.8 |
|
H1' |
C1' |
C2' |
C3' |
212.6 |
|
H1' |
C1' |
C2' |
SE |
328.3 |
|
H1' |
C1' |
C2' |
H2' |
89.8 |
|
C2' |
C1' |
H1' |
O4' |
120.9 |
|
O3' |
C3' |
C2' |
SE |
49.9 |
|
O3' |
C3' |
C2' |
H2' |
287.3 |
|
C2' |
C3' |
O3' |
C4' |
247.3 |
|
C2' |
C3' |
O3' |
H3' |
125.1 |
|
O3' |
C3' |
C4' |
H4' |
325.9 |
|
C4' |
C3' |
O3' |
H3' |
237.8 |
|
H3' |
C3' |
C2' |
SE |
168.0 |
|
H3' |
C3' |
C2' |
H2' |
45.4 |
|
C2' |
C3' |
H3' |
C4' |
116.2 |
|
C2' |
C3' |
H3' |
O3' |
239.7 |
|
H3' |
C3' |
C4' |
H4' |
207.5 |
|
C4' |
C3' |
H3' |
O3' |
123.6 |
|
H3' |
C3' |
O3' |
HO3' |
219.9 |
|
CA' |
SE |
C2' |
H2' |
315.1 |
|
HA'1 |
CA' |
SE |
HA'2 |
240.0 |
|
HA'1 |
CA' |
SE |
HA'3 |
119.9 |
|
HA'2 |
CA' |
SE |
HA'3 |
240.0 |
|
SE |
CA' |
HA'1 |
HA'2 |
120.0 |
|
SE |
CA' |
HA'1 |
HA'3 |
240.0 |
|
HA'2 |
CA' |
HA'1 |
HA'3 |
120.0 |
|
SE |
CA' |
HA'2 |
HA'1 |
240.0 |
|
SE |
CA' |
HA'2 |
HA'3 |
120.0 |
|
HA'1 |
CA' |
HA'2 |
HA'3 |
240.0 |
|
SE |
CA' |
HA'3 |
HA'1 |
120.0 |
|
SE |
CA' |
HA'3 |
HA'2 |
240.0 |
|
HA'1 |
CA' |
HA'3 |
HA'2 |
120.0 |
|
HO3' |
O3' |
C3' |
H3' |
219.9 |
|