PDB Chemical Component URX

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 URX

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP1 P 1.584 1.480
OP3 P 1.600 1.610
P O5' 1.543 1.610
P OP2 1.592 1.611
C1' N1 1.451 1.466
N1 C6 1.353 1.368
N1 C2 1.369 1.345
O2 C2 1.299 1.216
C2 N3 1.337 1.347
N3 C4 1.330 1.349
C5 C4 1.390 1.415
C4 O4 1.251 1.218
C6 C5 1.389 1.350
C5 H5 1.080 1.079
C6 H6 1.080 1.080
O4' C1' 1.442 1.440
C1' C2' 1.534 1.562
C1' H1' 1.100 1.090
C6' C2' 1.504 1.561
C3' C2' 1.453 1.572
C2' H2' 1.100 1.090
C4' C3' 1.489 1.569
O3' C3' 1.457 1.429
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.966
C5' C4' 1.496 1.530
C8' C4' 1.496 1.559
C4' O4' 1.453 1.454
C5' O5' 1.423 1.429
C5' H5' 1.100 1.091
C5' H5'A 1.100 1.090
C8' C6' 1.496 1.568
C7' C6' 1.476 1.530
C6' H6' 1.100 1.090
C7' H7' 1.100 1.091
C7' H7'A 1.100 1.090
C7' H7'B 1.100 1.089
C8' H8' 1.100 1.090
C8' H8'A 1.101 1.091
OP2 HOP2 0.951 0.966
OP3 HOP3 0.950 0.968
N3 HN3 1.000 0.970

Bond Angles for URX

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 112.0 109.5
O5' P OP2 109.3 109.5
P O5' C5' 117.6 123.0
P OP2 HOP2 109.5 114.0
C2 N1 C6 119.5 120.6
N1 C6 C5 119.7 119.7
N1 C6 H6 120.1 120.1
N1 C2 N3 120.9 120.9
O2 C2 N3 118.3 119.5
C2 N3 C4 121.1 120.2
C2 N3 HN3 119.4 119.9
N3 C4 O4 118.9 120.2
C4 N3 HN3 119.4 119.9
C6 C5 H5 120.7 120.4
O4' C1' H1' 113.5 110.3
C2' C1' H1' 111.7 110.2
C1' C2' H2' 114.3 116.7
C6' C2' H2' 113.8 116.6
C3' C2' H2' 119.6 117.0
C4' C3' H3' 118.2 112.3
O3' C3' H3' 103.8 111.9
O5' C5' H5' 110.1 109.4
O5' C5' H5'A 110.1 109.5
H5' C5' H5'A 108.9 109.4
C8' C6' H6' 112.7 110.4
C7' C6' H6' 102.0 110.5
H7' C7' H7'A 109.5 109.4
H7' C7' H7'B 109.4 109.5
H7'A C7' H7'B 109.5 109.5
H8' C8' H8'A 106.4 110.5

Torsion Angles for URX

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5' P OP1 OP2 120.4 120.0
OP1 P OP2 HOP2 0.0 180.0
OP3 P OP2 HOP2 112.6 300.0
OP1 P O5' OP2 237.9 240.0
O5' P OP2 HOP2 240.4 60.0
P O5' C5' H5' 33.0 60.0
P O5' C5' H5'A 272.9 300.1
OP2 P O5' C5' 173.2 65.0
C1' N1 C6 H6 1.4 0.2
C6 N1 C2 N3 359.3 359.9
N1 C6 C5 H5 181.8 180.0
C2 N1 C6 C5 358.1 0.1
C2 N1 C6 H6 178.1 180.0
O2 C2 N1 N3 181.5 180.1
N1 C2 N3 C4 3.5 0.0
N1 C2 N3 HN3 183.6 180.1
O2 C2 N1 C6 180.8 180.0
N1 C2 O2 N3 178.5 179.9
O2 C2 N3 C4 182.1 179.9
O2 C2 N3 HN3 2.1 360.0
N3 C2 N1 C6 359.3 359.9
C2 N3 C4 O4 179.4 180.0
C4 N3 C2 HN3 180.0 180.0
C2 N3 C4 HN3 180.0 180.0
N1 C6 C5 C4 1.8 360.0
C5 C4 N3 HN3 176.4 180.0
O4 C4 N3 HN3 359.3 360.0
N1 C6 C5 H6 180.0 179.9
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 H5 1.8 0.1
C2' C1' O4' H1' 238.4 240.9
O4' C1' C2' H2' 195.2 201.4
O4' C1' C2' H1' 122.8 119.1
C6' C2' C1' H2' 233.2 230.3
C3' C2' C1' H2' 129.0 126.4
H1' C1' C2' H2' 72.4 82.3
C6' C2' C1' H1' 305.6 312.6
C1' C2' C6' H2' 127.1 129.7
C3' C2' C6' H2' 230.9 231.7
C3' C2' C1' H1' 201.4 208.6
C1' C2' C3' H2' 234.6 233.9
C6' C2' C3' H2' 125.2 128.0
H2' C2' C1' H1' 72.4 82.3
C4' C3' C2' H2' 178.8 176.1
O3' C3' C4' H3' 119.8 127.3
O3' C3' C2' H2' 293.5 292.6
C4' C3' O3' H3' 231.9 232.6
H3' C3' C2' H2' 53.3 59.8
HO3' O3' C3' H3' 51.8 294.1
P O5' C5' C4' 152.9 180.0
C5' C4' C3' H3' 308.4 297.5
C8' C4' C3' H3' 182.0 171.2
C4' O4' C1' H1' 122.7 117.6
O4' C4' C3' H3' 70.5 63.6
C5' O5' P OP2 173.2 65.0
H5' C5' O5' H5'A 120.0 119.9
O5' C5' H5' H5'A 239.3 240.1
O5' C5' H5'A H5' 120.7 119.9
C8' C6' C2' H2' 166.6 164.0
C7' C6' C8' H6' 114.7 123.4
C7' C6' C2' H2' 290.5 283.4
C8' C6' C7' H6' 238.9 236.6
H6' C6' C2' H2' 45.1 46.1
H7' C7' C6' H6' 60.6 289.8
H7'A C7' H7' H7'B 120.0 120.0
H7'A C7' C6' H6' 180.7 49.7
H7' C7' H7'A H7'B 240.0 240.0
H7'B C7' C6' H6' 300.7 169.8
H7' C7' H7'B H7'A 120.0 120.0
H8' C8' C6' H6' 357.7 358.2
H8'A C8' C6' H6' 237.7 235.8
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 O4 359.3 360.0