PDB Chemical Component URU

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 URU

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C5' C4' 1.504 1.530
C5' O5' 1.442 1.429
OP1 P 1.484 1.480
C4' O4' 1.458 1.444
C4' C3' 1.523 1.549
P O5' 1.601 1.610
P OP2 1.489 1.610
O4' C1' 1.397 1.437
C6' C3' 1.529 1.530
C6' C 1.510 1.507
O2' C2' 1.440 1.429
C3' C2' 1.521 1.548
C1' C2' 1.535 1.542
C1' N1 1.470 1.465
NZ' C 1.402 1.348
NZ' CZ' 1.453 1.466
C O3 1.222 1.213
CZ' CY' 1.537 1.530
CY' OY' 1.472 1.437
CY' CX' 1.524 1.541
OY' CV' 1.406 1.444
N1 C6 1.374 1.369
N1 C2 1.373 1.345
C6 C5 1.342 1.350
OW' CW' 1.400 1.429
CV' CW' 1.531 1.550
CV' N11 1.480 1.465
O2 C2 1.213 1.215
C2 N3 1.346 1.346
OX' CX' 1.411 1.430
CX' CW' 1.521 1.547
C5 C4 1.433 1.416
N11 C16 1.381 1.369
N11 C12 1.376 1.345
C16 C15 1.352 1.350
N3 C4 1.373 1.349
C4 O4 1.222 1.218
O12 C12 1.238 1.215
C12 N13 1.361 1.347
C15 C14 1.421 1.416
N13 C14 1.382 1.348
C14 O14 1.228 1.218
C5' H2 1.100 1.090
C5' H3 1.100 1.090
C4' H4 1.100 1.090
C3' H5 1.100 1.090
C6' H6 1.100 1.090
C6' H7 1.100 1.089
C2' H8 1.100 1.090
O2' H9 0.949 0.967
C1' H10 1.100 1.090
C6 H11 1.080 1.079
C5 H12 1.080 1.080
N3 H13 1.000 0.969
OP2 H14 0.950 0.968
NZ' H15 1.000 0.970
CZ' H16 1.100 1.089
CZ' H17 1.101 1.090
CY' H18 1.100 1.090
CX' H19 1.100 1.090
OX' H20 0.950 0.967
CW' H21 1.100 1.090
OW' H22 0.950 0.967
CV' H23 1.100 1.090
C16 H24 1.080 1.080
C15 H25 1.080 1.081
N13 H26 1.000 0.969
P OP3   1.610
OP3 H1   0.967

Bond Angles for URU

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5' C4' O4' 108.6 110.6
C5' C4' C3' 117.7 110.6
C4' C5' H2 109.6 109.4
C4' C5' H3 109.6 109.5
C5' C4' H4 108.8 110.5
OP1 P O5' 109.6 109.5
OP1 P OP2 120.4 109.4
OP1 P OP3   109.5
C3' C4' O4' 103.5 103.5
C4' O4' C1' 110.3 107.0
O4' C4' H4 109.4 110.6
C4' C3' C2' 102.1 102.1
C3' C4' H4 108.6 110.8
C4' C3' H5 108.1 110.9
O5' P OP2 105.7 109.4
O5' P OP3   109.5
P OP2 H14 109.5 114.0
OP2 P OP3   109.5
O4' C1' N1 110.3 109.9
O4' C1' H10 110.9 110.0
C6' C3' C2' 116.3 110.8
C6' C3' H5 108.0 110.8
C6' C O3 124.5 120.0
C C6' H6 109.1 109.4
C C6' H7 109.1 109.5
O2' C2' H8 112.4 110.5
C2' C3' H5 108.1 110.9
C3' C2' H8 111.1 110.5
C1' C2' H8 110.9 110.5
C1' N1 C6 122.4 119.7
C1' N1 C2 117.1 119.7
N1 C1' H10 109.8 109.9
NZ' CZ' CY' 106.5 109.4
CZ' NZ' H15 118.2 120.0
NZ' CZ' H16 110.2 109.5
NZ' CZ' H17 110.2 109.5
CZ' CY' OY' 111.0 109.9
CZ' CY' CX' 110.9 109.9
CY' CZ' H16 110.2 109.5
CY' CZ' H17 110.2 109.4
CZ' CY' H18 110.2 109.9
CX' CY' OY' 103.0 107.3
CY' OY' CV' 111.0 107.0
OY' CY' H18 111.1 109.8
CY' CX' CW' 101.7 104.2
CX' CY' H18 110.4 110.0
CY' CX' H19 108.7 110.5
OY' CV' N11 108.9 110.6
OY' CV' H23 110.8 110.7
C6 N1 C2 120.5 120.6
N1 C6 C5 122.6 119.7
N1 C6 H11 118.7 120.2
N1 C2 N3 115.6 120.9
C6 C5 C4 119.5 119.1
C5 C6 H11 118.7 120.1
C6 C5 H12 120.2 120.4
OW' CW' H21 113.5 110.8
CV' CW' H21 111.4 110.9
CV' N11 C16 122.6 119.7
CV' N11 C12 115.8 119.7
N11 CV' H23 109.8 110.6
C2 N3 H13 116.0 119.9
OX' CX' CW' 118.6 110.5
OX' CX' H19 110.2 110.5
CW' CX' H19 108.7 110.5
CX' CW' H21 111.5 110.9
C5 C4 O4 124.2 120.3
C4 C5 H12 120.3 120.4
C16 N11 C12 121.6 120.6
N11 C16 C15 120.6 119.6
N11 C16 H24 119.7 120.2
N11 C12 N13 116.2 121.0
C16 C15 C14 120.6 119.2
C15 C16 H24 119.7 120.2
C16 C15 H25 119.7 120.4
N3 C4 O4 121.9 120.3
C12 N13 H26 117.2 119.9
C15 C14 O14 129.1 120.3
C14 C15 H25 119.7 120.5
N13 C14 O14 115.6 120.3
H2 C5' H3 109.5 109.5
H6 C6' H7 109.5 109.5
H16 CZ' H17 109.5 109.5
P OP3 H1   114.0

Torsion Angles for URU

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C3' C4' C5' O4' 117.1 114.1
C5' C4' O4' C1' 146.8 158.6
O4' C4' C5' H4 119.0 122.8
C5' C4' C3' C2' 203.6 204.5
C3' C4' C5' H4 236.0 237.0
C5' C4' C3' H5 317.5 322.7
H2 C5' C4' H3 239.8 120.0
C5' O5' P OP2 177.7 295.0
C5' O5' P OP3   175.0
O5' P OP1 OP2 122.9 240.1
O5' P OP1 OP3   120.1
OP1 P OP2 H14 360.0 180.0
OP2 P OP1 OP3   240.0
OP1 P OP3 H1   300.0
C5' C4' O4' C3' 125.9 118.5
O4' C4' C5' H2 54.2 306.4
O4' C4' C5' H3 174.4 186.4
C5' C4' O4' H4 241.4 237.2
O4' C4' C3' C2' 323.4 323.0
C3' C4' O4' H4 115.6 118.7
O4' C4' C3' H5 77.3 81.2
C4' O4' C1' N1 244.2 214.1
C4' O4' C1' H10 122.4 93.0
C5' C4' C3' O4' 240.2 241.5
C3' C4' C5' H2 171.3 60.5
C3' C4' C5' H3 291.5 300.5
C5' C4' C3' H4 124.1 122.9
C3' C4' O4' C1' 20.9 40.0
O4' C4' C3' H4 243.8 241.4
C6' C3' C4' C2' 233.8 241.8
C6' C3' C4' H5 120.0 123.6
C2' C3' C4' H5 246.2 241.8
C4' C3' C2' H8 155.3 139.5
OP1 P O5' OP2 228.7 119.9
OP1 P O5' OP3   240.0
O5' P OP2 H14 235.2 300.0
OP2 P O5' OP3   120.0
O5' P OP3 H1   179.9
OP1 P OP2 O5' 124.8 240.0
OP1 P OP2 OP3   120.0
O5' P OP2 OP3   240.0
OP2 P OP3 H1   59.9
C1' O4' C4' H4 265.4 281.4
O4' C1' C2' H8 215.9 243.4
O4' C1' N1 C6 18.2 232.8
O4' C1' N1 C2 196.9 52.6
N1 C1' O4' H10 121.8 121.1
C6' C3' C4' O4' 197.3 204.8
C4' C3' C6' C2' 118.3 112.7
C6' C3' C4' H4 313.4 323.4
C4' C3' C6' H5 240.0 236.3
C2' C3' C6' H5 121.7 123.6
C6' C3' C2' H8 279.9 257.8
C C6' C3' C2' 59.4 72.3
C C6' C3' H5 297.7 308.7
H6 C6' C H7 119.6 120.0
O2' C2' C3' H5 165.6 143.9
C3' C2' O2' H8 236.6 237.4
C1' C2' O2' H8 125.8 122.6
C2' C3' C4' O4' 323.4 323.0
C2' C3' C4' H4 79.6 81.6
C4' C3' C2' H5 113.8 118.2
C6' C3' C2' H5 238.4 236.5
O2' C2' C3' H8 124.1 122.6
C1' C2' C3' H8 242.3 241.3
C4' O4' C1' C2' 3.4 333.5
O2' C2' C1' H8 233.5 237.4
C1' C2' C3' H5 283.8 262.6
C3' C2' C1' H8 117.9 118.7
O4' C1' N1 H10 237.6 238.9
N1 C1' C2' H8 335.7 2.8
C6 N1 C1' C2 181.3 180.2
C1' N1 C6 C5 179.3 180.0
C1' N1 C6 H11 359.3 360.0
C1' N1 C2 N3 180.3 179.8
NZ' C C6' H6 81.6 60.1
NZ' C C6' H7 322.0 300.0
NZ' CZ' CY' OY' 47.9 66.5
NZ' CZ' CY' CX' 161.7 184.3
CY' CZ' NZ' H16 240.5 240.0
CY' CZ' NZ' H17 119.5 119.9
NZ' CZ' CY' H18 284.3 305.5
H16 CZ' NZ' H17 239.1 239.9
O3 C C6' H6 260.6 240.0
O3 C C6' H7 141.1 120.0
CY' CZ' NZ' H15 71.0 360.0
NZ' CZ' CY' H16 119.5 120.0
NZ' CZ' CY' H17 240.5 240.0
CX' CY' CZ' OY' 113.9 117.8
CZ' CY' OY' CV' 142.2 145.9
OY' CY' CZ' H18 123.6 121.0
CZ' CY' CX' CW' 204.7 238.6
CX' CY' CZ' H18 237.4 238.8
CZ' CY' CX' H19 319.3 357.3
H16 CZ' CY' H17 121.0 120.0
CZ' CY' OY' CX' 118.8 119.4
OY' CY' CZ' H16 288.3 306.4
OY' CY' CZ' H17 167.4 186.4
CZ' CY' OY' H18 237.0 239.0
OY' CY' CX' CW' 323.5 358.0
CX' CY' OY' H18 118.2 119.6
OY' CY' CX' H19 78.1 116.7
CY' OY' CV' N11 239.1 201.4
CY' OY' CV' H23 118.2 78.5
CZ' CY' CX' OY' 241.2 240.6
CX' CY' CZ' H16 42.2 64.3
CX' CY' CZ' H17 281.3 304.2
CZ' CY' CX' H18 122.5 121.1
CX' CY' OY' CV' 23.4 26.5
OY' CY' CX' H18 241.3 240.5
OX' CX' CY' CW' 234.3 241.3
OX' CX' CY' H19 119.7 122.6
CW' CX' CY' H19 245.4 241.3
CY' CX' CW' H21 156.2 97.3
CV' OY' CY' H18 265.2 266.9
OY' CV' CW' H21 216.9 278.8
OY' CV' N11 C16 5.5 229.1
OY' CV' N11 C12 188.4 48.9
N11 CV' OY' H23 120.8 122.9
C1' N1 C6 C2 178.7 179.8
C6 N1 C1' H10 140.7 354.0
C6 N1 C2 N3 359.1 359.5
N1 C6 C5 C4 0.1 359.9
C5 C6 N1 H11 180.0 180.1
N1 C6 C5 H12 180.1 180.0
C1' N1 C2 C6 181.2 180.2
C2 N1 C1' H10 319.4 173.7
C2 N1 C6 C5 0.6 0.3
C2 N1 C6 H11 180.6 180.2
N1 C2 N3 H13 180.7 180.2
C5 C6 N1 C2 0.6 0.3
N1 C6 C5 H11 180.0 179.9
C6 C5 C4 O4 180.1 180.0
C4 C5 C6 H12 180.0 179.9
CV' CW' OW' H21 125.0 123.6
OW' CW' CX' H19 166.6 102.2
CX' CW' OW' H21 236.3 236.3
CY' OY' CV' CW' 359.9 320.0
OW' CW' CV' H21 233.8 236.5
CV' CW' CX' H19 281.9 220.4
CX' CW' CV' H21 119.8 118.2
OY' CV' N11 H23 238.5 237.0
N11 CV' CW' H21 335.6 37.3
C16 N11 CV' C12 177.2 180.2
CV' N11 C16 C15 183.3 180.0
CV' N11 C16 H24 3.4 0.0
CV' N11 C12 N13 177.5 179.8
O2 C2 N3 H13 0.3 360.0
C2 N3 C4 O4 179.5 179.8
OX' CX' CY' OY' 197.8 239.3
CY' CX' OX' CW' 115.0 114.8
OX' CX' CY' H18 316.5 358.7
CY' CX' OX' H19 241.2 237.5
CW' CX' OX' H19 126.2 122.6
OX' CX' CW' H21 274.7 216.0
CW' CX' CY' OY' 323.5 358.0
CW' CX' CY' H18 82.2 117.4
CY' CX' CW' H19 114.6 118.7
OW' CW' CX' H21 124.9 123.6
CV' CW' CX' H21 240.3 241.8
OX' CX' CW' H19 233.1 237.4
C4 C5 C6 H11 180.1 180.0
C6 C5 C4 H12 180.0 180.1
N3 C4 C5 O4 179.5 180.1
CV' N11 C16 C12 183.0 179.8
C16 N11 CV' H23 127.0 352.1
C16 N11 C12 N13 0.3 359.6
N11 C16 C15 C14 359.1 0.0
C15 C16 N11 H24 180.0 179.9
N11 C16 C15 H25 179.1 179.9
CV' N11 C12 C16 177.2 180.2
C12 N11 CV' H23 309.9 171.9
C12 N11 C16 C15 0.4 0.2
C12 N11 C16 H24 180.4 180.2
N11 C12 N13 H26 179.5 180.2
C15 C16 N11 C12 0.4 0.2
N11 C16 C15 H24 180.0 180.1
C16 C15 C14 O14 180.0 180.0
C14 C15 C16 H25 180.0 180.1
N1 C2 N3 C4 0.7 0.5
C5 C4 N3 O4 180.5 179.9
N3 C4 C5 H12 179.6 180.0
O4 C4 C5 H12 0.1 359.9
O12 C12 N13 H26 359.8 0.1
C12 N13 C14 O14 180.6 179.8
C14 C15 C16 H24 179.0 180.0
C16 C15 C14 H25 180.0 179.9
N13 C14 C15 O14 180.8 180.0
N11 C12 N13 C14 359.6 0.5
C15 C14 N13 O14 179.3 180.0
N13 C14 C15 H25 180.8 180.1
O14 C14 C15 H25 360.0 0.1
H2 C5' C4' O4' 54.2 306.4
H2 C5' C4' C3' 171.3 60.5
C4' C5' H2 H3 120.2 240.0
H2 C5' C4' H4 295.2 183.6
H3 C5' C4' O4' 174.4 186.4
H3 C5' C4' C3' 291.5 300.5
C4' C5' H3 H2 239.7 120.0
H3 C5' C4' H4 55.4 63.6
C5' C4' H4 O4' 118.5 122.9
C5' C4' H4 C3' 230.8 237.0
H4 C4' C5' H2 295.2 183.6
H4 C4' C5' H3 55.4 63.6
C3' C4' H4 O4' 247.7 245.8
H4 C4' O4' C1' 265.4 281.4
H4 C4' C3' C2' 79.6 81.6
H4 C4' C3' H5 193.4 199.7
H5 C3' C4' O4' 77.3 81.2
C4' C3' H5 C2' 250.2 247.2
H5 C3' C4' H4 193.4 199.7
C6' C3' H5 C2' 126.6 123.5
H5 C3' C2' H8 41.5 21.3
H6 C6' C3' C2' 179.6 192.2
H6 C6' C3' H5 58.0 68.7
H6 C6' C O3 260.6 240.0
C C6' H6 H7 240.6 240.0
H7 C6' C3' C2' 299.2 312.2
H7 C6' C3' H5 177.5 188.7
H7 C6' C O3 141.1 120.0
C C6' H7 H6 119.3 120.0
H8 C2' C3' H5 41.5 21.3
H9 O2' C2' H8 303.4 302.6
O4' C1' H10 N1 122.1 121.1
H10 C1' C2' H8 95.8 123.8
H10 C1' N1 C6 140.7 354.0
H10 C1' N1 C2 319.4 173.7
H11 C6 N1 C2 180.6 180.2
N1 C6 H11 C5 180.0 180.1
H11 C6 C5 C4 180.1 180.0
H11 C6 C5 H12 0.1 0.1
C6 C5 H12 C4 180.0 179.9
H12 C5 C6 H11 0.1 0.1
H12 C5 C4 O4 0.1 359.9
H13 N3 C4 O4 359.5 0.1
H14 OP2 P OP3   60.0
H15 NZ' CZ' CY' 71.0 360.0
H15 NZ' CZ' H16 190.5 120.0
H15 NZ' CZ' H17 311.4 240.0
NZ' CZ' H16 CY' 242.7 240.0
H16 CZ' NZ' H15 190.5 120.0
NZ' CZ' H16 H17 121.3 120.0
H16 CZ' CY' OY' 288.3 306.4
H16 CZ' CY' CX' 42.2 64.3
CY' CZ' H16 H17 238.6 240.0
H16 CZ' CY' H18 164.8 185.4
NZ' CZ' H17 CY' 117.2 119.9
H17 CZ' NZ' H15 311.4 240.0
NZ' CZ' H17 H16 238.6 239.9
H17 CZ' CY' OY' 167.4 186.4
H17 CZ' CY' CX' 281.3 304.2
CY' CZ' H17 H16 121.4 120.0
H17 CZ' CY' H18 43.8 65.4
CZ' CY' H18 OY' 123.5 121.0
CZ' CY' H18 CX' 237.1 238.9
H18 CY' CZ' H16 164.8 185.4
H18 CY' CZ' H17 43.8 65.4
CX' CY' H18 OY' 246.4 242.1
H18 CY' OY' CV' 265.2 266.9
H18 CY' CX' CW' 82.2 117.4
H18 CY' CX' H19 196.8 236.2
H19 CX' CY' OY' 78.1 116.7
CY' CX' H19 CW' 250.1 245.2
H19 CX' CY' H18 196.8 236.2
OX' CX' H19 CW' 131.6 122.6
H19 CX' CW' H21 41.6 338.6
H20 OX' CX' CW' 65.0 65.2
H20 OX' CX' H19 298.8 302.6
H21 CW' CX' H19 41.6 338.6
H22 OW' CW' H21 54.9 62.2
OY' CV' H23 N11 120.3 123.0
H23 CV' CW' H21 97.4 160.2
H23 CV' N11 C16 127.0 352.1
H23 CV' N11 C12 309.9 171.9
H24 C16 N11 C12 180.4 180.2
N11 C16 H24 C15 180.0 179.9
H24 C16 C15 C14 179.0 180.0
H24 C16 C15 H25 359.0 359.9
C16 C15 H25 C14 180.0 180.1
H25 C15 C16 H24 359.0 359.9
H25 C15 C14 O14 360.0 0.1
H26 N13 C14 O14 0.6 0.0
OP1 P OP3 O5'   120.0
OP1 P OP3 OP2   240.0
O5' P OP3 OP2   120.0
OP3 P OP2 H14   60.0