PDB Chemical Component PST

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 PST

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.515 1.610
P OP2 1.592 1.609
P SP 1.881 1.862
P O5' 1.595 1.610
OP1 HOP1 0.949 0.967
OP2 HOP2 0.950 0.967
O5' C5' 1.436 1.428
C5' C4' 1.494 1.530
C5' H5' 1.115 1.090
C5' H5'' 1.116 1.090
C4' O4' 1.415 1.445
C4' C3' 1.484 1.550
C4' H4' 1.115 1.090
O4' C1' 1.438 1.437
C3' O3' 1.434 1.429
C3' C2' 1.498 1.548
C3' H3' 1.115 1.090
O3' HO3 0.949 0.967
C2' C1' 1.501 1.541
C2' H2' 1.115 1.089
C2' H2'' 1.115 1.089
C1' N1 1.490 1.465
C1' H1' 1.115 1.090
N1 C2 1.390 1.344
N1 C6 1.396 1.368
C2 O2 1.224 1.216
C2 N3 1.345 1.347
N3 C4 1.377 1.349
N3 HN3 1.019 0.969
C4 O4 1.209 1.218
C4 C5 1.451 1.415
C5 C5M 1.535 1.507
C5 C6 1.353 1.350
C5M H71 1.116 1.090
C5M H72 1.114 1.090
C5M H73 1.115 1.090
C6 H6 1.103 1.080

Bond Angles for PST

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 104.2 109.4
OP1 P SP 118.6 109.4
OP1 P O5' 102.9 109.5
P OP1 HOP1 104.1 106.8
OP2 P SP 113.7 109.5
OP2 P O5' 99.2 109.5
P OP2 HOP2 104.2 106.9
SP P O5' 115.8 109.5
P O5' C5' 119.0 106.8
O5' C5' C4' 113.2 109.5
O5' C5' H5' 110.9 109.4
O5' C5' H5'' 110.8 109.5
C4' C5' H5' 110.9 109.5
C4' C5' H5'' 110.9 109.5
C5' C4' O4' 108.8 110.7
C5' C4' C3' 110.9 110.6
C5' C4' H4' 107.5 110.5
H5' C5' H5'' 99.4 109.5
O4' C4' C3' 104.6 103.6
O4' C4' H4' 113.5 110.5
C4' O4' C1' 107.5 106.8
C3' C4' H4' 111.6 110.6
C4' C3' O3' 112.0 110.9
C4' C3' C2' 100.1 102.1
C4' C3' H3' 114.5 110.9
O4' C1' C2' 106.2 107.5
O4' C1' N1 104.8 109.9
O4' C1' H1' 117.3 109.9
O3' C3' C2' 111.3 110.9
O3' C3' H3' 104.0 110.8
C3' O3' HO3 112.1 106.8
C2' C3' H3' 115.3 110.9
C3' C2' C1' 100.8 104.2
C3' C2' H2' 115.5 110.5
C3' C2' H2'' 115.5 110.5
C1' C2' H2' 115.5 110.5
C1' C2' H2'' 115.5 110.5
C2' C1' N1 116.8 109.9
C2' C1' H1' 105.4 109.8
H2' C2' H2'' 95.0 110.5
N1 C1' H1' 106.8 109.9
C1' N1 C2 116.0 119.7
C1' N1 C6 123.4 119.6
C2 N1 C6 120.6 120.6
N1 C2 O2 125.6 119.5
N1 C2 N3 116.9 120.9
N1 C6 C5 121.9 119.7
N1 C6 H6 120.7 120.2
O2 C2 N3 117.5 119.5
C2 N3 C4 125.5 120.2
C2 N3 HN3 116.0 119.9
C4 N3 HN3 118.5 119.9
N3 C4 O4 117.2 120.3
N3 C4 C5 116.8 119.4
O4 C4 C5 126.0 120.3
C4 C5 C5M 121.4 120.4
C4 C5 C6 118.2 119.1
C5M C5 C6 120.5 120.5
C5 C5M H71 121.4 109.5
C5 C5M H72 108.0 109.5
C5 C5M H73 108.0 109.5
C5 C6 H6 117.4 120.1
H71 C5M H72 108.0 109.4
H71 C5M H73 107.9 109.5
H72 C5M H73 102.0 109.5

Torsion Angles for PST

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 SP 127.6 120.0
OP2 P OP1 O5' 256.9 240.0
OP1 P OP2 HOP2 180.0 60.0
SP P OP1 O5' 129.3 120.0
OP1 P O5' C5' 192.7 180.0
OP1 P OP2 SP 229.5 240.0
OP1 P OP2 O5' 105.9 120.0
OP2 P OP1 HOP1 179.9 60.0
SP P OP2 O5' 236.4 239.9
OP2 P O5' C5' 299.6 299.9
OP1 P SP OP2 122.9 120.0
OP1 P SP O5' 236.9 240.0
SP P OP1 HOP1 52.4 300.0
OP2 P SP O5' 114.0 120.1
SP P OP2 HOP2 310.5 180.0
SP P O5' C5' 61.7 60.0
OP1 P O5' OP2 253.1 240.1
OP1 P O5' SP 131.0 120.0
O5' P OP1 HOP1 283.1 180.0
OP2 P O5' SP 237.9 239.9
O5' P OP2 HOP2 74.1 300.0
P O5' C5' C4' 168.0 180.0
P O5' C5' H5' 293.4 60.0
P O5' C5' H5'' 42.7 300.0
HOP1 OP1 P OP2 179.9 60.0
HOP1 OP1 P SP 52.4 300.0
HOP1 OP1 P O5' 283.1 180.0
HOP2 OP2 P SP 310.5 180.0
HOP2 OP2 P O5' 74.1 300.0
C4' C5' O5' H5' 234.7 120.0
C4' C5' O5' H5'' 125.3 240.0
O5' C5' C4' O4' 304.9 65.7
O5' C5' C4' C3' 59.3 180.0
O5' C5' C4' H4' 181.5 302.9
H5' C5' O5' H5'' 250.7 120.0
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.7 120.0
H5' C5' C4' H5'' 109.4 240.0
O4' C4' C5' C3' 245.5 245.7
O4' C4' C5' H4' 123.3 122.8
C5' C4' O4' C1' 144.6 158.5
C3' C4' C5' H4' 237.8 237.1
C5' C4' C3' O3' 81.6 86.1
C5' C4' C3' C2' 199.7 204.3
C5' C4' C3' H3' 323.5 322.5
O5' C5' H5' C4' 233.4 120.0
O5' C5' H5' H5'' 116.7 240.0
C4' C5' H5' H5'' 243.3 120.0
H5' C5' C4' O4' 179.5 185.7
H5' C5' C4' C3' 294.0 300.0
H5' C5' C4' H4' 56.2 62.9
O5' C5' H5'' C4' 126.6 240.0
O5' C5' H5'' H5' 243.3 120.0
C4' C5' H5'' H5' 116.7 240.0
H5'' C5' C4' O4' 70.2 305.7
H5'' C5' C4' C3' 184.6 60.0
H5'' C5' C4' H4' 306.8 182.9
O4' C4' C5' H5' 179.5 185.7
O4' C4' C5' H5'' 70.2 305.7
C5' C4' O4' C3' 118.5 118.6
C5' C4' O4' H4' 240.4 237.2
C3' C4' O4' H4' 121.9 118.6
O4' C4' C3' O3' 198.7 204.8
O4' C4' C3' C2' 316.8 323.0
O4' C4' C3' H3' 80.6 81.2
C4' O4' C1' C2' 1.8 333.7
C4' O4' C1' N1 237.6 214.2
C4' O4' C1' H1' 119.3 93.2
C3' C4' C5' H5' 294.0 300.0
C3' C4' C5' H5'' 184.6 60.0
C5' C4' C3' O4' 242.9 241.3
C5' C4' C3' H4' 119.8 122.8
O4' C4' C3' H4' 236.9 241.5
C3' C4' O4' C1' 26.1 39.9
O3' C3' C4' C2' 242.0 241.8
O3' C3' C4' H3' 118.1 123.6
C4' C3' O3' HO3 180.0 174.1
C2' C3' C4' H3' 236.1 241.8
C4' C3' C2' C1' 42.6 20.9
C4' C3' C2' H2' 167.9 262.2
C4' C3' C2' H2'' 277.4 139.5
H4' C4' C5' H5' 56.2 62.9
H4' C4' C5' H5'' 306.8 182.9
C5' C4' H4' O4' 120.4 122.9
C5' C4' H4' C3' 238.2 237.1
O4' C4' H4' C3' 117.9 114.2
H4' C4' O4' C1' 264.2 281.3
H4' C4' C3' O3' 321.9 323.3
H4' C4' C3' C2' 79.9 81.5
H4' C4' C3' H3' 203.8 199.6
C1' O4' C4' C3' 26.1 39.9
C1' O4' C4' H4' 264.2 281.3
C3' C2' C1' O4' 331.7 1.9
O4' C1' C2' H2' 206.4 120.6
O4' C1' C2' H2'' 96.9 243.3
C2' C1' O4' N1 124.2 119.5
C2' C1' O4' H1' 242.5 240.5
N1 C1' O4' H1' 118.3 121.0
O4' C1' N1 C2 197.7 58.3
O4' C1' N1 C6 17.0 238.3
O3' C3' C4' H4' 321.9 323.3
C4' C3' O3' C2' 111.1 112.7
C4' C3' O3' H3' 235.8 236.3
C2' C3' O3' H3' 124.7 123.6
O3' C3' C2' C1' 161.2 139.1
O3' C3' C2' H2' 286.5 20.4
O3' C3' C2' H2'' 36.0 257.8
C2' C3' C4' H4' 79.9 81.5
C4' C3' C2' O3' 241.4 241.8
C4' C3' C2' H3' 123.3 118.2
O4' C1' C2' C3' 331.7 1.9
O3' C3' C2' H3' 241.9 236.4
C2' C3' O3' HO3 68.9 61.4
C1' C2' C3' H2' 234.7 118.7
C1' C2' C3' H2'' 125.2 241.4
C3' C2' C1' N1 88.1 121.4
C3' C2' C1' H1' 206.5 242.4
H2' C2' C3' H2'' 250.5 122.6
H3' C3' C4' H4' 203.8 199.6
C4' C3' H3' O3' 122.6 123.7
C4' C3' H3' C2' 244.7 247.3
O3' C3' H3' C2' 122.1 123.6
H3' C3' O3' HO3 304.2 297.8
H3' C3' C2' C1' 279.3 262.7
H3' C3' C2' H2' 44.6 144.0
H3' C3' C2' H2'' 154.1 21.4
HO3 O3' C3' C2' 68.9 61.4
HO3 O3' C3' H3' 304.2 297.8
O4' C1' C2' N1 243.6 240.5
O4' C1' C2' H1' 125.2 119.5
C1' C2' C3' H3' 279.3 262.7
C3' C2' C1' H2' 125.3 241.3
C3' C2' C1' H2'' 234.8 118.6
H2' C2' C1' H2'' 109.5 237.3
N1 C1' C2' H1' 241.6 239.0
C2' C1' N1 C2 80.5 300.3
C2' C1' N1 C6 259.7 120.2
H2' C2' C3' H3' 44.6 144.0
C3' C2' H2' C1' 242.7 114.8
C3' C2' H2' H2'' 121.4 237.4
C1' C2' H2' H2'' 238.6 122.6
H2' C2' C1' N1 322.8 240.1
H2' C2' C1' H1' 81.3 1.1
H2'' C2' C3' H3' 154.1 21.4
C3' C2' H2'' C1' 117.2 245.3
C3' C2' H2'' H2' 238.6 122.6
C1' C2' H2'' H2' 121.4 237.3
H2'' C2' C1' N1 213.3 2.8
H2'' C2' C1' H1' 331.7 123.8
O4' C1' N1 C2' 117.2 118.0
O4' C1' N1 H1' 234.9 238.9
N1 C1' C2' H2' 322.8 240.1
N1 C1' C2' H2'' 213.3 2.8
C2' C1' N1 H1' 117.7 120.9
C2 N1 C1' C6 180.7 180.0
C1' N1 C2 O2 358.7 0.1
C1' N1 C2 N3 179.0 180.0
C1' N1 C6 C5 180.9 180.0
C1' N1 C6 H6 0.8 0.1
O4' C1' H1' C2' 242.1 242.0
O4' C1' H1' N1 117.1 121.0
H1' C1' C2' H2' 81.3 1.1
H1' C1' C2' H2'' 331.7 123.8
C2' C1' H1' N1 235.1 239.1
H1' C1' N1 C2 322.8 179.4
H1' C1' N1 C6 142.1 359.3
C2 N1 C1' H1' 322.8 179.4
C1' N1 C2 C6 179.3 180.0
C2 N1 C6 C5 0.1 359.9
C2 N1 C6 H6 180.1 180.0
O2 C2 N1 N3 179.7 180.1
N1 C2 N3 C4 0.2 359.8
N1 C2 N3 HN3 180.2 180.0
C6 N1 C1' H1' 142.1 359.3
C1' N1 C6 C2 180.8 180.0
C6 N1 C2 O2 179.4 180.1
C6 N1 C2 N3 359.7 0.0
C4 C5 C6 N1 0.2 0.3
C5M C5 C6 N1 181.1 180.0
C5 C6 N1 H6 180.1 179.9
O2 C2 N1 C6 179.4 180.1
N1 C2 O2 N3 180.3 179.9
O2 C2 N3 C4 180.4 179.7
O2 C2 N3 HN3 0.4 359.9
N3 C2 N1 C6 359.7 0.0
N1 C2 N3 O2 179.8 180.1
C4 N3 C2 HN3 180.0 179.8
C2 N3 C4 O4 181.2 180.0
C2 N3 C4 C5 0.2 0.4
C2 N3 C4 HN3 180.0 180.2
O4 C4 N3 C5 181.0 179.6
N3 C4 C5 C5M 178.7 179.8
N3 C4 C5 C6 359.7 359.6
C2 N3 HN3 C4 180.0 179.8
HN3 N3 C4 O4 1.2 359.8
HN3 N3 C4 C5 180.1 180.2
O4 C4 N3 HN3 1.2 359.8
N3 C4 O4 C5 178.9 180.4
O4 C4 C5 C5M 357.6 0.2
O4 C4 C5 C6 178.5 179.9
N1 C6 C5 C4 0.2 0.3
C5 C4 N3 HN3 180.1 180.2
N3 C4 C5 O4 181.1 179.6
C5M C5 C4 C6 179.1 180.3
C4 C5 C5M H71 180.0 359.7
C4 C5 C5M H72 305.3 119.7
C4 C5 C5M H73 54.8 239.7
C4 C5 C6 H6 180.3 180.2
N1 C6 C5 C5M 181.1 180.0
C4 C5 C5M C6 180.9 179.7
C5M C5 C6 H6 1.2 359.9
H71 C5M C5 H72 234.7 240.0
H71 C5M C5 H73 125.2 120.0
H72 C5M C5 H73 250.5 240.0
N1 C6 C5 H6 179.9 180.1
C4 C5 C6 C5M 179.1 180.3
C6 C5 C5M H71 359.1 180.0
C6 C5 C5M H72 124.3 300.0
C6 C5 C5M H73 233.9 60.0
H71 C5M C5 C6 359.1 180.0
C5 C5M H71 H72 125.3 120.0
C5 C5M H71 H73 234.8 240.0
H72 C5M H71 H73 109.5 120.0
H72 C5M C5 C6 124.3 300.0
C5 C5M H72 H71 227.1 240.0
C5 C5M H72 H73 113.6 120.0
H71 C5M H72 H73 246.5 240.0
H73 C5M C5 C6 233.9 60.0
C5 C5M H73 H71 132.9 120.0
C5 C5M H73 H72 246.4 240.0
H71 C5M H73 H72 113.5 119.9
N1 C6 H6 C5 180.1 179.9