PDB Chemical Component DSZ
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 DSZ
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| CA |
C |
1.502 |
1.507 |
| C |
NAT |
1.338 |
1.348 |
| C |
O |
1.224 |
1.212 |
| N |
CA |
1.457 |
1.469 |
| N |
HN |
0.999 |
1.009 |
| N |
HNA |
1.000 |
1.009 |
| C2 |
N1 |
1.352 |
1.321 |
| N1 |
C6 |
1.346 |
1.330 |
| N3 |
C2 |
1.345 |
1.317 |
| C2 |
H2 |
1.080 |
1.080 |
| N3 |
C4 |
1.347 |
1.328 |
| N9 |
C4 |
1.329 |
1.372 |
| C4 |
C5 |
1.462 |
1.406 |
| C5 |
N7 |
1.343 |
1.355 |
| C5 |
C6 |
1.463 |
1.404 |
| C6 |
N6 |
1.348 |
1.384 |
| N6 |
HN6 |
1.000 |
0.970 |
| N6 |
HN6A |
1.000 |
0.970 |
| C8 |
N7 |
1.349 |
1.302 |
| N9 |
C8 |
1.351 |
1.364 |
| C8 |
H8 |
1.080 |
1.080 |
| C1' |
N9 |
1.472 |
1.465 |
| CA |
CB |
1.533 |
1.530 |
| CA |
HA |
1.100 |
1.090 |
| CB |
CG |
1.523 |
1.506 |
| CB |
HB |
1.100 |
1.090 |
| CB |
HBA |
1.100 |
1.090 |
| CG |
OD2 |
1.255 |
1.208 |
| CG |
OD1 |
1.257 |
1.343 |
| O4' |
C1' |
1.428 |
1.444 |
| C1' |
C2' |
1.517 |
1.550 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
C2' |
1.516 |
1.548 |
| C2' |
O2' |
1.430 |
1.429 |
| C2' |
H2' |
1.100 |
1.091 |
| O2' |
HO2' |
0.950 |
0.967 |
| C4' |
C3' |
1.523 |
1.541 |
| O3' |
C3' |
1.426 |
1.429 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.949 |
0.967 |
| C5' |
C4' |
1.514 |
1.530 |
| C4' |
O4' |
1.439 |
1.438 |
| C4' |
H4' |
1.100 |
1.090 |
| C5' |
O5' |
1.423 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.090 |
| SBE |
O5' |
1.621 |
1.523 |
| NAT |
SBE |
1.538 |
1.656 |
| NAT |
HNAT |
1.000 |
0.970 |
| OAX |
SBE |
1.471 |
1.420 |
| SBE |
OAY |
1.472 |
1.421 |
| OD1 |
HOD1 |
0.950 |
0.967 |
Bond Angles for DSZ
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
C |
NAT |
115.3 |
120.0 |
| O |
C |
NAT |
124.5 |
120.0 |
| C |
NAT |
SBE |
125.0 |
120.0 |
| C |
NAT |
HNAT |
117.5 |
120.0 |
| CA |
N |
HN |
109.5 |
111.1 |
| CA |
N |
HNA |
109.5 |
111.0 |
| N |
CA |
CB |
112.8 |
109.5 |
| N |
CA |
HA |
107.1 |
109.5 |
| HN |
N |
HNA |
109.4 |
111.0 |
| C2 |
N1 |
C6 |
121.6 |
121.2 |
| N1 |
C6 |
C5 |
118.0 |
118.5 |
| N1 |
C6 |
N6 |
122.9 |
120.7 |
| N3 |
C2 |
H2 |
117.9 |
118.7 |
| N3 |
C4 |
C5 |
120.7 |
119.1 |
| C4 |
C5 |
N7 |
107.4 |
107.1 |
| C4 |
C5 |
C6 |
116.7 |
118.2 |
| C6 |
C5 |
N7 |
135.9 |
134.7 |
| C5 |
C6 |
N6 |
119.1 |
120.8 |
| C6 |
N6 |
HN6 |
109.5 |
120.0 |
| C6 |
N6 |
HN6A |
109.4 |
120.0 |
| HN6 |
N6 |
HN6A |
109.5 |
120.0 |
| N9 |
C8 |
H8 |
124.7 |
125.0 |
| CB |
CA |
HA |
106.3 |
109.5 |
| CA |
CB |
CG |
114.5 |
109.4 |
| CA |
CB |
HB |
107.8 |
109.5 |
| CA |
CB |
HBA |
107.9 |
109.5 |
| CG |
CB |
HB |
107.8 |
109.5 |
| CG |
CB |
HBA |
107.8 |
109.4 |
| CB |
CG |
OD2 |
120.5 |
120.0 |
| CB |
CG |
OD1 |
117.7 |
120.0 |
| HB |
CB |
HBA |
111.0 |
109.5 |
| OD1 |
CG |
OD2 |
121.8 |
120.0 |
| CG |
OD1 |
HOD1 |
109.5 |
117.0 |
| O4' |
C1' |
H1' |
114.7 |
110.7 |
| C2' |
C1' |
H1' |
109.7 |
110.6 |
| C1' |
C2' |
O2' |
112.1 |
110.9 |
| C1' |
C2' |
H2' |
114.4 |
110.9 |
| C3' |
C2' |
H2' |
112.6 |
110.9 |
| O2' |
C2' |
H2' |
102.5 |
110.8 |
| C2' |
O2' |
HO2' |
109.5 |
114.0 |
| C4' |
C3' |
H3' |
116.4 |
110.5 |
| O3' |
C3' |
H3' |
108.9 |
110.4 |
| C5' |
C4' |
H4' |
106.2 |
110.0 |
| O4' |
C4' |
H4' |
112.2 |
109.8 |
| O5' |
C5' |
H5' |
110.6 |
109.5 |
| O5' |
C5' |
H5'A |
110.5 |
109.5 |
| H5' |
C5' |
H5'A |
108.4 |
109.5 |
| SBE |
NAT |
HNAT |
117.5 |
120.0 |
| NAT |
SBE |
OAX |
106.5 |
106.4 |
| NAT |
SBE |
OAY |
111.8 |
106.4 |
| OAX |
SBE |
OAY |
111.3 |
123.2 |
Torsion Angles for DSZ
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O |
C |
CA |
NAT |
180.5 |
179.8 |
| CA |
C |
NAT |
SBE |
180.6 |
179.7 |
| CA |
C |
NAT |
HNAT |
0.6 |
359.8 |
| SBE |
NAT |
C |
HNAT |
180.0 |
179.9 |
| C |
NAT |
SBE |
OAX |
160.4 |
311.5 |
| C |
NAT |
SBE |
OAY |
282.2 |
178.6 |
| CA |
C |
O |
NAT |
179.5 |
180.2 |
| O |
C |
NAT |
SBE |
0.1 |
359.9 |
| O |
C |
NAT |
HNAT |
180.1 |
180.0 |
| N |
CA |
C |
NAT |
154.9 |
160.0 |
| HN |
N |
CA |
HNA |
240.0 |
236.0 |
| CB |
CA |
N |
HA |
116.6 |
120.1 |
| N |
CA |
CB |
CG |
52.3 |
295.0 |
| N |
CA |
CB |
HB |
172.3 |
55.0 |
| N |
CA |
CB |
HBA |
292.3 |
175.0 |
| CA |
N |
HN |
HNA |
120.0 |
124.0 |
| HN |
N |
CA |
CB |
55.1 |
176.1 |
| HN |
N |
CA |
HA |
298.5 |
56.0 |
| CA |
N |
HNA |
HN |
240.0 |
236.0 |
| HNA |
N |
CA |
CB |
175.1 |
300.0 |
| HNA |
N |
CA |
HA |
58.5 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
0.4 |
0.0 |
| C2 |
N1 |
C6 |
N6 |
180.6 |
180.0 |
| C4 |
C5 |
C6 |
N1 |
0.1 |
0.0 |
| N1 |
C6 |
C5 |
N7 |
180.0 |
180.0 |
| C5 |
C6 |
N1 |
N6 |
179.8 |
180.0 |
| N1 |
C6 |
N6 |
HN6 |
360.0 |
360.0 |
| N1 |
C6 |
N6 |
HN6A |
120.0 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
359.8 |
359.9 |
| H2 |
C2 |
N1 |
C6 |
179.7 |
179.9 |
| C4 |
N3 |
C2 |
H2 |
179.7 |
180.0 |
| N3 |
C4 |
C5 |
N7 |
179.4 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.3 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
0.1 |
0.0 |
| C6 |
C5 |
C4 |
N7 |
180.0 |
180.0 |
| C4 |
C5 |
C6 |
N6 |
179.9 |
180.0 |
| C4 |
C5 |
N7 |
C6 |
179.9 |
179.9 |
| N7 |
C5 |
C6 |
N6 |
359.8 |
360.0 |
| N1 |
C6 |
C5 |
N6 |
180.2 |
180.0 |
| C4 |
C5 |
C6 |
N7 |
180.1 |
180.1 |
| C5 |
C6 |
N6 |
HN6 |
180.2 |
180.0 |
| C5 |
C6 |
N6 |
HN6A |
300.2 |
0.0 |
| N1 |
C6 |
N6 |
C5 |
179.8 |
180.0 |
| N6 |
C6 |
C5 |
N7 |
359.8 |
360.0 |
| HN6 |
N6 |
C6 |
HN6A |
240.0 |
179.9 |
| C6 |
N6 |
HN6 |
HN6A |
120.0 |
180.1 |
| C6 |
N6 |
HN6A |
HN6 |
240.0 |
179.9 |
| C1' |
N9 |
C8 |
H8 |
1.2 |
0.0 |
| CB |
CA |
C |
NAT |
280.8 |
279.9 |
| CB |
CA |
N |
HN |
55.1 |
176.1 |
| CB |
CA |
N |
HNA |
175.1 |
300.0 |
| N |
CA |
CB |
HA |
242.9 |
240.0 |
| CG |
CB |
CA |
HB |
240.0 |
240.0 |
| CG |
CB |
CA |
HBA |
120.0 |
119.9 |
| CA |
CB |
CG |
OD2 |
354.3 |
0.0 |
| CA |
CB |
CG |
OD1 |
174.8 |
180.0 |
| HB |
CB |
CA |
HBA |
240.0 |
239.9 |
| HA |
CA |
C |
NAT |
37.6 |
40.0 |
| HA |
CA |
N |
HN |
298.5 |
56.0 |
| HA |
CA |
N |
HNA |
58.5 |
180.0 |
| N |
CA |
HA |
CB |
120.8 |
120.0 |
| HA |
CA |
CB |
CG |
169.4 |
55.0 |
| HA |
CA |
CB |
HB |
289.4 |
175.0 |
| HA |
CA |
CB |
HBA |
49.4 |
295.1 |
| CG |
CB |
CA |
HA |
169.4 |
55.0 |
| CA |
CB |
CG |
HB |
120.0 |
120.0 |
| CA |
CB |
CG |
HBA |
240.0 |
240.0 |
| HB |
CB |
CG |
HBA |
120.0 |
120.1 |
| OD1 |
CG |
CB |
OD2 |
180.5 |
180.0 |
| CB |
CG |
OD1 |
HOD1 |
179.4 |
180.0 |
| HB |
CB |
CA |
HA |
289.4 |
175.0 |
| CA |
CB |
HB |
CG |
235.9 |
240.0 |
| CA |
CB |
HB |
HBA |
118.0 |
120.0 |
| CG |
CB |
HB |
HBA |
242.1 |
240.0 |
| HB |
CB |
CG |
OD2 |
234.3 |
240.0 |
| HB |
CB |
CG |
OD1 |
54.8 |
60.0 |
| HBA |
CB |
CA |
HA |
49.4 |
295.1 |
| CA |
CB |
HBA |
CG |
124.1 |
119.9 |
| CA |
CB |
HBA |
HB |
242.1 |
240.0 |
| CG |
CB |
HBA |
HB |
117.9 |
120.0 |
| HBA |
CB |
CG |
OD2 |
114.3 |
120.0 |
| HBA |
CB |
CG |
OD1 |
294.9 |
300.0 |
| OD2 |
CG |
CB |
HB |
234.3 |
240.0 |
| OD2 |
CG |
CB |
HBA |
114.3 |
120.0 |
| CB |
CG |
OD2 |
OD1 |
180.6 |
180.0 |
| OD2 |
CG |
OD1 |
HOD1 |
360.0 |
360.0 |
| OD1 |
CG |
CB |
HB |
54.8 |
60.0 |
| OD1 |
CG |
CB |
HBA |
294.9 |
300.0 |
| CB |
CG |
OD1 |
OD2 |
179.5 |
180.0 |
| C2' |
C1' |
O4' |
H1' |
240.0 |
241.4 |
| O4' |
C1' |
C2' |
H2' |
276.8 |
278.8 |
| O4' |
C1' |
C2' |
H1' |
123.3 |
118.6 |
| C3' |
C2' |
C1' |
H2' |
121.8 |
118.2 |
| O2' |
C2' |
C1' |
H2' |
243.9 |
236.5 |
| C1' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
| H1' |
C1' |
C2' |
O2' |
37.3 |
36.6 |
| H1' |
C1' |
C2' |
H2' |
153.5 |
160.1 |
| C3' |
C2' |
C1' |
H1' |
275.3 |
278.3 |
| C1' |
C2' |
C3' |
H2' |
237.0 |
241.8 |
| O2' |
C2' |
C3' |
H2' |
116.2 |
123.6 |
| C3' |
C2' |
O2' |
HO2' |
294.9 |
292.8 |
| O2' |
C2' |
C1' |
H1' |
37.3 |
36.6 |
| C1' |
C2' |
O2' |
H2' |
123.2 |
123.6 |
| C3' |
C2' |
O2' |
H2' |
238.0 |
236.3 |
| H2' |
C2' |
C1' |
H1' |
153.5 |
160.1 |
| C1' |
C2' |
H2' |
O2' |
238.5 |
236.4 |
| H2' |
C2' |
O2' |
HO2' |
56.8 |
56.4 |
| HO2' |
O2' |
C2' |
H2' |
56.8 |
56.4 |
| C4' |
C3' |
C2' |
H2' |
94.3 |
97.3 |
| O3' |
C3' |
C4' |
H3' |
120.7 |
122.5 |
| O3' |
C3' |
C2' |
H2' |
207.6 |
216.1 |
| C4' |
C3' |
O3' |
H3' |
234.6 |
237.4 |
| H3' |
C3' |
C2' |
H2' |
329.0 |
338.6 |
| HO3' |
O3' |
C3' |
H3' |
58.1 |
298.9 |
| C5' |
C4' |
C3' |
H3' |
9.9 |
357.3 |
| O4' |
C4' |
C5' |
H4' |
121.4 |
121.1 |
| C4' |
O4' |
C1' |
H1' |
86.1 |
78.6 |
| O4' |
C4' |
C3' |
H3' |
130.7 |
116.7 |
| C5' |
C4' |
O4' |
H4' |
242.2 |
238.9 |
| H4' |
C4' |
C3' |
H3' |
252.2 |
236.1 |
| O5' |
C5' |
C4' |
H4' |
168.9 |
306.1 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
288.9 |
66.1 |
| O5' |
C5' |
H5' |
H5'A |
238.7 |
239.9 |
| H5'A |
C5' |
C4' |
H4' |
48.9 |
186.1 |
| O5' |
C5' |
H5'A |
H5' |
121.3 |
120.1 |
| C |
NAT |
SBE |
O5' |
41.3 |
65.0 |
| SBE |
O5' |
C5' |
H5' |
25.2 |
60.0 |
| SBE |
O5' |
C5' |
H5'A |
265.2 |
300.0 |
| C |
NAT |
SBE |
HNAT |
180.0 |
180.1 |
| OAX |
SBE |
NAT |
OAY |
238.3 |
132.9 |
| C |
NAT |
HNAT |
SBE |
180.0 |
179.9 |
| HNAT |
NAT |
SBE |
OAX |
340.4 |
131.4 |
| HNAT |
NAT |
SBE |
OAY |
102.1 |
358.5 |
| OAX |
SBE |
NAT |
HNAT |
340.4 |
131.4 |
| NAT |
SBE |
OAX |
OAY |
122.0 |
237.0 |
| OAY |
SBE |
NAT |
HNAT |
102.1 |
358.5 |
| NAT |
SBE |
OAY |
OAX |
241.0 |
123.0 |
| HOD1 |
OD1 |
CG |
OD2 |
360.0 |
360.0 |