PDB Chemical Component KAG

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 KAG

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.611 1.617
OP1 P 1.484 1.618
P OP2 1.484 1.501
P O5' 1.608 1.620
O5' C5' 1.421 1.416
C5' C4' 1.537 1.522
C5' H5' 1.100 1.092
C5' H5'' 1.100 1.091
C4' O4' 1.430 1.443
C4' C3' 1.534 1.526
C4' H4' 1.100 1.095
O4' C1' 1.423 1.437
C3' O3' 1.424 1.426
C3' C2' 1.529 1.511
C3' H3' 1.100 1.092
C2' C1' 1.528 1.523
C2' H2'' 1.100 1.096
C2' H2' 1.100 1.095
C1' N9 1.486 1.459
C1' H1' 1.100 1.095
N9 C4 1.378 1.366
N9 C8 1.374 1.376
C4 N3 1.366 1.352
C4 C5 1.379 1.374
N3 C2 1.340 1.315
C8 N7 1.309 1.319
C8 H8 1.080 1.082
N7 C5 1.404 1.363
C5 C6 1.443 1.437
C6 O6 1.232 1.224
C6 N1 1.380 1.402
N1 C2 1.359 1.415
N1 H1 1.000 1.015
C2 N2 1.322 1.370
N2 C1A 1.458 1.433
N2 H2 1.000 0.990
C1A C1M 1.527 1.524
C1A C2B 1.530 1.529
C1A H1A 1.100 1.097
C1M H1M 1.100 1.096
C1M H2M 1.100 1.095
C1M H3M 1.100 1.095
C2B C3G 1.518 1.513
C2B H2B 1.100 1.096
C2B H1B 1.100 1.097
C3G O2G 1.234 1.226
C3G H3G 1.080 1.104
HO1 OP3 0.950 0.981
HO2 OP1 0.950 0.981
HO3 O3' 0.950 0.970

Bond Angles for KAG

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP1 108.8 103.3
OP3 P OP2 109.7 115.3
OP3 P O5' 100.0 103.7
OP1 P OP2 119.3 115.0
OP1 P O5' 109.3 102.9
OP2 P O5' 108.0 115.0
P O5' C5' 121.0 118.5
O5' C5' C4' 111.0 108.7
O5' C5' H5' 108.6 109.2
O5' C5' H5'' 109.0 109.2
C4' C5' H5' 108.6 110.1
C4' C5' H5'' 108.9 110.1
C5' C4' O4' 110.0 108.1
C5' C4' C3' 110.5 112.7
C5' C4' H4' 107.7 109.4
H5' C5' H5'' 110.7 109.6
O4' C4' C3' 107.2 106.8
O4' C4' H4' 111.0 107.8
C4' O4' C1' 110.0 108.8
C3' C4' H4' 110.5 112.0
C4' C3' O3' 109.1 109.6
C4' C3' C2' 101.7 103.2
C4' C3' H3' 116.2 113.9
O4' C1' C2' 106.3 106.7
O4' C1' N9 110.3 110.0
O4' C1' H1' 112.3 108.1
O3' C3' C2' 113.7 108.4
O3' C3' H3' 104.7 107.8
C2' C3' H3' 111.7 113.8
C3' C2' C1' 102.2 101.6
C3' C2' H2'' 112.0 110.1
C3' C2' H2' 113.5 114.2
C1' C2' H2'' 112.0 110.5
C1' C2' H2' 113.5 111.7
C2' C1' N9 113.1 114.3
C2' C1' H1' 109.5 111.7
H2'' C2' H2' 104.0 108.7
N9 C1' H1' 105.5 105.9
C1' N9 C4 126.2 127.4
C1' N9 C8 128.5 126.1
C4 N9 C8 105.3 106.5
N9 C4 N3 126.6 126.0
N9 C4 C5 106.5 105.0
N9 C8 N7 114.4 112.5
N9 C8 H8 122.8 121.9
N3 C4 C5 126.9 129.1
C4 N3 C2 113.6 113.0
C4 C5 N7 110.2 112.1
C4 C5 C6 117.8 119.2
N3 C2 N1 123.5 122.6
N3 C2 N2 121.0 122.0
N7 C8 H8 122.8 125.6
C8 N7 C5 103.5 103.9
N7 C5 C6 131.9 128.7
C5 C6 O6 129.5 123.8
C5 C6 N1 113.7 110.8
O6 C6 N1 116.8 125.4
C6 N1 C2 124.4 125.3
C6 N1 H1 117.8 117.4
C2 N1 H1 117.8 117.4
N1 C2 N2 115.4 115.3
C2 N2 C1A 125.3 120.5
C2 N2 H2 117.4 116.5
C1A N2 H2 117.3 123.0
N2 C1A C1M 109.7 108.6
N2 C1A C2B 109.4 110.0
N2 C1A H1A 110.3 108.5
C1M C1A C2B 112.2 111.0
C1M C1A H1A 107.5 108.8
C1A C1M H1M 109.5 111.4
C1A C1M H2M 109.5 110.8
C1A C1M H3M 109.5 111.0
C2B C1A H1A 107.7 109.9
C1A C2B C3G 111.5 113.6
C1A C2B H2B 108.8 111.1
C1A C2B H1B 108.3 110.2
H1M C1M H2M 109.4 107.4
H1M C1M H3M 109.5 108.1
H2M C1M H3M 109.5 107.9
C3G C2B H2B 108.8 107.4
C3G C2B H1B 108.3 106.4
C2B C3G O2G 120.6 124.9
C2B C3G H3G 119.7 114.8
H2B C2B H1B 111.1 107.9
O2G C3G H3G 119.7 120.3

Torsion Angles for KAG

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 227.9 233.7
OP1 P OP3 O5' 114.5 107.1
OP2 P OP3 O5' 246.7 233.4
OP3 P O5' C5' 70.9 53.2
OP3 P OP1 OP2 126.8 126.5
OP3 P OP1 O5' 251.7 252.3
OP2 P OP1 O5' 124.9 125.8
OP1 P O5' C5' 316.8 305.8
OP3 P OP2 OP1 233.6 239.9
OP3 P OP2 O5' 108.1 120.6
OP1 P OP2 O5' 234.5 240.7
OP2 P O5' C5' 185.6 180.1
OP3 P O5' OP1 114.2 107.4
OP3 P O5' OP2 245.4 233.2
OP1 P O5' OP2 131.2 125.8
P O5' C5' C4' 206.5 180.0
P O5' C5' H5' 87.2 300.1
P O5' C5' H5'' 326.5 59.8
C4' C5' O5' H5' 119.4 239.9
C4' C5' O5' H5'' 240.0 120.2
O5' C5' C4' O4' 74.7 61.8
O5' C5' C4' C3' 192.9 179.5
O5' C5' C4' H4' 313.6 304.7
H5' C5' O5' H5'' 120.7 240.3
O5' C5' C4' H5' 240.6 119.5
O5' C5' C4' H5'' 120.0 240.4
H5' C5' C4' H5'' 239.4 120.9
O4' C4' C5' C3' 241.9 242.3
O4' C4' C5' H4' 121.1 117.1
C5' C4' O4' C1' 113.1 116.0
C3' C4' C5' H4' 239.2 234.8
C5' C4' C3' O3' 146.1 152.1
C5' C4' C3' C2' 266.6 267.4
C5' C4' C3' H3' 28.1 31.2
O5' C5' H5' C4' 120.9 240.8
O5' C5' H5' H5'' 240.4 119.5
C4' C5' H5' H5'' 119.6 238.7
H5' C5' C4' O4' 194.1 302.3
H5' C5' C4' C3' 312.2 60.0
H5' C5' C4' H4' 73.0 185.2
O5' C5' H5'' C4' 238.7 119.3
O5' C5' H5'' H5' 119.4 240.5
C4' C5' H5'' H5' 240.7 121.2
H5'' C5' C4' O4' 314.7 181.4
H5'' C5' C4' C3' 72.9 299.1
H5'' C5' C4' H4' 193.6 64.3
O4' C4' C5' H5' 194.1 302.3
O4' C4' C5' H5'' 314.7 181.4
C5' C4' O4' C3' 120.2 121.5
C5' C4' O4' H4' 240.9 241.9
C3' C4' O4' H4' 120.7 120.5
O4' C4' C3' O3' 266.0 270.6
O4' C4' C3' C2' 26.4 25.9
O4' C4' C3' H3' 148.0 149.7
C4' O4' C1' C2' 344.3 342.7
C4' O4' C1' N9 221.4 218.2
C4' O4' C1' H1' 104.1 103.0
C3' C4' C5' H5' 312.2 60.0
C3' C4' C5' H5'' 72.9 299.1
C5' C4' C3' O4' 240.2 241.5
C5' C4' C3' H4' 119.1 123.8
O4' C4' C3' H4' 238.9 242.3
C3' C4' O4' C1' 353.0 354.5
O3' C3' C4' C2' 239.5 244.7
O3' C3' C4' H3' 118.0 120.8
C2' C3' C4' H3' 238.4 236.2
C4' C3' C2' C1' 325.7 325.2
C4' C3' C2' H2'' 85.7 82.3
C4' C3' C2' H2' 203.0 204.8
H4' C4' C5' H5' 73.0 185.2
H4' C4' C5' H5'' 193.6 64.3
C5' C4' H4' O4' 120.5 117.2
C5' C4' H4' C3' 239.2 234.4
O4' C4' H4' C3' 118.8 117.1
H4' C4' O4' C1' 232.2 234.1
H4' C4' C3' O3' 27.0 28.3
H4' C4' C3' C2' 147.5 143.6
H4' C4' C3' H3' 269.0 267.5
C1' O4' C4' C3' 353.0 354.5
C1' O4' C4' H4' 232.2 234.1
C3' C2' C1' O4' 31.7 32.8
O4' C1' C2' H2'' 271.7 276.0
O4' C1' C2' H2' 154.3 154.9
C2' C1' O4' N9 122.9 124.5
C2' C1' O4' H1' 240.2 239.7
N9 C1' O4' H1' 117.4 115.2
O4' C1' N9 C4 227.5 213.5
O4' C1' N9 C8 45.3 33.4
O3' C3' C4' H4' 27.0 28.3
C4' C3' O3' C2' 112.7 111.9
C4' C3' O3' H3' 235.0 235.5
C2' C3' O3' H3' 122.3 123.6
O3' C3' C2' C1' 82.8 81.3
O3' C3' C2' H2'' 202.8 198.4
O3' C3' C2' H2' 320.2 320.9
C2' C3' C4' H4' 147.5 143.6
C4' C3' C2' O3' 242.9 243.9
C4' C3' C2' H3' 124.6 123.9
O4' C1' C2' C3' 31.7 32.8
O3' C3' C2' H3' 241.7 240.1
C1' C2' C3' H2'' 240.0 242.9
C1' C2' C3' H2' 122.6 120.4
C3' C2' C1' N9 152.8 154.6
C3' C2' C1' H1' 270.1 274.8
H2'' C2' C3' H2' 242.6 237.5
H3' C3' C4' H4' 269.0 267.5
C4' C3' H3' O3' 120.4 121.8
C4' C3' H3' C2' 243.9 242.1
O3' C3' H3' C2' 123.6 120.3
H3' C3' C2' C1' 201.1 201.3
H3' C3' C2' H2'' 321.1 318.4
H3' C3' C2' H2' 78.4 80.9
O4' C1' C2' N9 238.9 238.2
O4' C1' C2' H1' 121.6 117.9
C1' C2' C3' H3' 201.1 201.3
C3' C2' C1' H2'' 120.0 116.8
C3' C2' C1' H2' 237.4 237.9
H2'' C2' C1' H2' 117.4 121.1
N9 C1' C2' H1' 242.7 239.8
C2' C1' N9 C4 108.7 93.5
C2' C1' N9 C8 286.5 273.4
H2'' C2' C3' H3' 321.1 318.4
C3' C2' H2'' C1' 245.9 248.5
C3' C2' H2'' H2' 122.9 125.7
C1' C2' H2'' H2' 237.1 237.1
H2'' C2' C1' N9 32.8 37.8
H2'' C2' C1' H1' 150.1 158.0
H2' C2' C3' H3' 78.4 80.9
C3' C2' H2' C1' 116.2 114.6
C3' C2' H2' H2'' 238.1 236.7
C1' C2' H2' H2'' 121.9 122.1
H2' C2' C1' N9 275.5 276.7
H2' C2' C1' H1' 32.8 37.0
O4' C1' N9 C2' 118.8 120.0
O4' C1' N9 H1' 238.5 243.4
N9 C1' C2' H2'' 32.8 37.8
N9 C1' C2' H2' 275.5 276.7
C2' C1' N9 H1' 119.7 123.4
C4 N9 C1' C8 182.2 180.0
C1' N9 C4 N3 355.9 359.9
C1' N9 C4 C5 175.3 180.0
C1' N9 C8 N7 184.1 180.0
C1' N9 C8 H8 4.1 0.0
O4' C1' H1' C2' 242.1 242.9
O4' C1' H1' N9 120.2 117.9
H1' C1' C2' H2'' 150.1 158.0
H1' C1' C2' H2' 32.8 37.0
C2' C1' H1' N9 238.0 235.0
H1' C1' N9 C4 349.0 330.0
H1' C1' N9 C8 166.8 150.0
C4 N9 C1' H1' 349.0 330.0
C1' N9 C4 C8 178.2 180.0
C4 N9 C8 N7 2.3 360.0
C4 N9 C8 H8 182.3 180.0
N3 C4 N9 C5 180.6 179.9
N9 C4 N3 C2 178.9 180.0
N9 C4 C5 N7 2.7 360.0
N9 C4 C5 C6 182.5 180.0
C8 N9 C1' H1' 166.8 150.0
C1' N9 C8 C4 181.8 180.0
C8 N9 C4 N3 177.7 179.9
C8 N9 C4 C5 357.1 0.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.4 0.0
N3 C4 N9 C8 177.7 179.9
N9 C4 N3 C5 179.2 180.1
N3 C4 C5 N7 182.1 180.1
N3 C4 C5 C6 1.9 0.1
C4 N3 C2 N1 358.8 0.0
C4 N3 C2 N2 176.2 180.0
C5 C4 N9 C8 357.1 0.0
N9 C4 C5 N3 180.6 179.9
C5 C4 N3 C2 359.7 359.9
C8 N7 C5 C4 358.7 360.0
N7 C5 C4 C6 180.2 180.0
C4 C5 C6 O6 178.3 179.9
C4 C5 C6 N1 358.2 360.0
C2 N3 C4 C5 359.7 359.9
C6 N1 C2 N3 1.1 0.0
N3 C2 N1 H1 181.1 180.0
N1 C2 N3 N2 182.6 180.0
N3 C2 N2 C1A 350.8 0.0
N3 C2 N2 H2 170.8 180.0
N9 C8 N7 H8 180.0 180.0
C4 C5 N7 C8 358.7 360.0
C8 N7 C5 C6 178.9 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 179.4 180.0
C4 C5 N7 C6 179.7 180.0
C5 N7 C8 H8 179.4 180.0
N7 C5 C6 O6 358.0 359.9
N7 C5 C6 N1 177.9 180.0
C4 C5 C6 N7 180.3 180.0
O6 C6 C5 N1 180.1 179.9
C5 C6 N1 C2 0.5 360.0
C5 C6 N1 H1 180.5 180.0
C5 C6 O6 N1 179.9 180.1
O6 C6 N1 C2 180.4 180.0
O6 C6 N1 H1 0.4 0.0
N3 C2 N1 C6 1.1 0.0
C5 C6 N1 O6 180.1 179.9
C2 N1 C6 H1 180.0 180.0
C6 N1 C2 N2 183.5 180.0
N3 C2 N1 N2 177.5 180.0
C6 N1 C2 H1 180.0 180.0
N1 C2 N2 C1A 168.4 180.0
N1 C2 N2 H2 348.4 360.0
C6 N1 H1 C2 180.0 180.0
H1 N1 C2 N2 3.5 0.0
N3 C2 N2 N1 182.4 180.0
N2 C2 N1 H1 3.5 0.0
C1A N2 C2 H2 180.0 180.0
C2 N2 C1A C1M 89.9 78.1
C2 N2 C1A C2B 213.5 199.7
C2 N2 C1A H1A 331.8 320.0
C2 N2 C1A H2 180.0 180.0
C1M C1A N2 C2B 236.5 238.4
C1M C1A N2 H1A 118.2 118.1
N2 C1A C1M H1M 72.3 61.2
N2 C1A C1M H2M 312.3 301.6
N2 C1A C1M H3M 192.3 181.7
C2B C1A N2 H1A 241.7 239.7
N2 C1A C2B C3G 176.7 59.4
N2 C1A C2B H2B 296.7 298.3
N2 C1A C2B H1B 57.6 178.7
C2 N2 H2 C1A 180.0 180.0
H2 N2 C1A C1M 269.9 258.1
H2 N2 C1A C2B 33.4 19.8
H2 N2 C1A H1A 151.7 140.1
C1M C1A N2 H2 269.9 258.1
N2 C1A C1M C2B 121.9 121.0
N2 C1A C1M H1A 240.1 242.1
C2B C1A C1M H1A 118.2 121.0
C1M C1A C2B C3G 298.7 179.7
C1M C1A C2B H2B 58.7 58.5
C1M C1A C2B H1B 179.6 298.9
H1M C1M C1A H2M 120.0 119.6
H1M C1M C1A H3M 240.0 239.5
H2M C1M C1A H3M 120.0 119.9
C2B C1A N2 H2 33.4 19.8
N2 C1A C2B C1M 238.0 239.8
N2 C1A C2B H1A 119.9 119.4
C1M C1A C2B H1A 241.9 239.7
C2B C1A C1M H1M 310.4 300.2
C2B C1A C1M H2M 190.4 180.6
C2B C1A C1M H3M 70.4 60.7
C3G C2B C1A H2B 240.0 121.2
C3G C2B C1A H1B 119.1 240.7
C1A C2B C3G O2G 121.2 356.8
C1A C2B C3G H3G 301.2 176.2
H2B C2B C1A H1B 239.1 119.6
H1A C1A N2 H2 151.7 140.1
N2 C1A H1A C1M 119.5 118.0
N2 C1A H1A C2B 240.6 239.7
C1M C1A H1A C2B 121.1 121.7
H1A C1A C1M H1M 192.2 179.1
H1A C1A C1M H2M 72.2 59.5
H1A C1A C1M H3M 312.2 299.7
H1A C1A C2B C3G 56.8 300.0
H1A C1A C2B H2B 176.8 178.8
H1A C1A C2B H1B 297.7 59.3
H1M C1M C1A C2B 310.4 300.2
H1M C1M C1A H1A 192.2 179.1
C1A C1M H1M H2M 240.0 238.4
C1A C1M H1M H3M 120.0 122.2
H2M C1M H1M H3M 240.0 243.8
H2M C1M C1A C2B 190.4 180.6
H2M C1M C1A H1A 72.2 59.5
C1A C1M H2M H1M 120.0 122.0
C1A C1M H2M H3M 240.0 238.3
H1M C1M H2M H3M 120.0 116.3
H3M C1M C1A C2B 70.4 60.7
H3M C1M C1A H1A 312.2 299.7
C1A C1M H3M H1M 240.0 237.5
C1A C1M H3M H2M 120.0 121.6
H1M C1M H3M H2M 240.0 244.1
C3G C2B C1A H1A 56.8 300.0
C1A C2B C3G H2B 120.0 236.8
C1A C2B C3G H1B 240.9 121.4
H2B C2B C3G H1B 120.9 244.7
O2G C3G C2B H3G 180.0 180.6
H2B C2B C1A H1A 176.8 178.8
C1A C2B H2B C3G 238.3 124.7
C1A C2B H2B H1B 119.2 239.1
C3G C2B H2B H1B 240.9 114.3
H2B C2B C3G O2G 1.2 120.0
H2B C2B C3G H3G 181.2 299.5
H1B C2B C1A H1A 297.7 59.3
C1A C2B H1B C3G 121.1 236.5
C1A C2B H1B H2B 240.6 121.5
C3G C2B H1B H2B 119.4 245.0
H1B C2B C3G O2G 240.3 235.4
H1B C2B C3G H3G 60.3 54.8
O2G C3G C2B H2B 1.2 120.0
O2G C3G C2B H1B 240.3 235.4
C2B C3G O2G H3G 180.0 179.4
H3G C3G C2B H2B 181.2 299.5
H3G C3G C2B H1B 60.3 54.8
C2B C3G H3G O2G 180.0 180.5