PDB Chemical Component GEK

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 GEK

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C O 1.252 1.220
C CA 1.508 1.507
C OXT 1.236 1.219
N CA 1.516 1.469
N HN 1.000 1.009
N HNA 1.001 1.009
N1 C2 1.388 1.321
N1 C6 1.325 1.329
C2 N3 1.363 1.316
C2 H2 1.080 1.079
N3 C4 1.315 1.329
C4 C5 1.377 1.404
C4 N9 1.390 1.371
C5 C6 1.365 1.405
C5 N7 1.324 1.355
C6 N6 1.462 1.384
N6 HN6 1.000 0.970
N6 HN6A 1.000 0.970
N7 C8 1.351 1.302
C8 N9 1.377 1.363
C8 H8 1.080 1.080
N9 C1' 1.473 1.466
CA CB 1.535 1.529
CA HA 1.100 1.090
CB CG 1.537 1.530
CB HB 1.100 1.091
CB HBA 1.100 1.089
SD CE 1.788 1.815
SD CG 1.813 1.813
SD C5' 1.811 1.815
CE CZ 1.510 1.506
CE HE 1.100 1.090
CE HEA 1.100 1.089
CG HG 1.100 1.090
CG HGA 1.100 1.090
CZ OZ1 1.327 1.219
CZ OZ2 1.344 1.220
C1' C2' 1.500 1.550
C1' O4' 1.420 1.444
C1' H1' 1.100 1.089
C2' O2' 1.403 1.430
C2' C3' 1.509 1.548
C2' H2' 1.101 1.090
O2' HO2' 0.950 0.967
C3' O3' 1.429 1.429
C3' C4' 1.506 1.541
C3' H3' 1.100 1.090
O3' HO3' 0.951 0.967
C4' O4' 1.445 1.437
C4' C5' 1.538 1.530
C4' H4' 1.100 1.090
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
N H22 1.000 1.009

Bond Angles for GEK

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O C CA 114.1 120.0
O C OXT 129.5 120.0
CA C OXT 116.4 120.0
C CA N 111.1 109.4
C CA CB 109.7 109.5
C CA HA 107.9 109.5
CA N HN 109.5 109.4
CA N HNA 109.5 109.5
N CA CB 112.5 109.5
N CA HA 107.8 109.4
CA N H22 109.4 109.5
HN N HNA 109.4 109.4
HN N H22 109.5 109.5
HNA N H22 109.5 109.5
C2 N1 C6 123.9 121.2
N1 C2 N3 116.5 122.4
N1 C2 H2 121.8 118.8
N1 C6 C5 118.3 118.5
N1 C6 N6 119.5 120.8
N3 C2 H2 121.8 118.8
C2 N3 C4 120.2 120.7
N3 C4 C5 122.8 119.0
N3 C4 N9 131.4 134.9
C5 C4 N9 105.7 106.0
C4 C5 C6 118.1 118.2
C4 C5 N7 110.6 107.1
C4 N9 C8 106.7 107.4
C4 N9 C1' 123.2 126.3
C6 C5 N7 130.8 134.7
C5 C6 N6 122.2 120.8
C5 N7 C8 107.4 109.4
C6 N6 HN6 109.5 120.0
C6 N6 HN6A 109.4 120.0
HN6 N6 HN6A 109.5 120.0
N7 C8 N9 109.2 110.0
N7 C8 H8 125.4 125.0
N9 C8 H8 125.4 125.0
C8 N9 C1' 129.7 126.3
N9 C1' C2' 115.4 110.6
N9 C1' O4' 105.2 110.6
N9 C1' H1' 110.6 110.6
CB CA HA 107.6 109.5
CA CB CG 111.6 109.5
CA CB HB 109.0 109.5
CA CB HBA 108.9 109.5
CG CB HB 108.9 109.4
CG CB HBA 109.0 109.5
CB CG SD 109.7 109.5
CB CG HG 109.4 109.5
CB CG HGA 109.4 109.5
HB CB HBA 109.4 109.5
CE SD CG 103.3 103.0
CE SD C5' 106.6 103.0
SD CE CZ 112.4 109.4
SD CE HE 108.7 109.4
SD CE HEA 108.8 109.4
CG SD C5' 99.8 103.0
SD CG HG 109.4 109.5
SD CG HGA 109.4 109.4
SD C5' C4' 110.6 109.5
SD C5' H5' 109.2 109.4
SD C5' H5'A 109.2 109.5
CZ CE HE 108.7 109.5
CZ CE HEA 108.7 109.5
CE CZ OZ1 114.0 120.0
CE CZ OZ2 119.0 120.0
HE CE HEA 109.5 109.5
HG CG HGA 109.5 109.5
OZ1 CZ OZ2 125.3 120.0
C2' C1' O4' 103.9 103.5
C2' C1' H1' 110.1 110.6
C1' C2' O2' 113.5 110.9
C1' C2' C3' 101.6 102.1
C1' C2' H2' 108.1 111.0
O4' C1' H1' 111.3 110.8
C1' O4' C4' 103.4 107.0
O2' C2' C3' 115.8 110.9
O2' C2' H2' 109.4 110.8
C2' O2' HO2' 109.5 114.0
C3' C2' H2' 108.0 110.9
C2' C3' O3' 112.3 110.5
C2' C3' C4' 103.2 104.1
C2' C3' H3' 108.5 110.5
O3' C3' C4' 114.3 110.5
O3' C3' H3' 109.6 110.5
C3' O3' HO3' 109.5 114.0
C4' C3' H3' 108.5 110.6
C3' C4' O4' 108.0 107.3
C3' C4' C5' 111.7 109.8
C3' C4' H4' 110.1 109.9
O4' C4' C5' 106.3 109.9
O4' C4' H4' 111.0 109.9
C5' C4' H4' 109.7 110.0
C4' C5' H5' 109.2 109.5
C4' C5' H5'A 109.2 109.5
H5' C5' H5'A 109.5 109.5

Torsion Angles for GEK

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
CA C O OXT 181.2 180.2
O C CA N 160.4 170.0
O C CA CB 285.5 290.1
O C CA HA 42.4 50.1
O C CA OXT 179.0 179.8
C CA N HN 180.0 180.1
C CA N HNA 300.0 299.9
N CA C CB 235.0 240.0
N CA C HA 118.0 119.9
C CA N H22 60.0 60.0
CB CA C HA 243.1 240.0
C CA CB CG 189.8 175.0
C CA CB HB 310.1 295.0
C CA CB HBA 69.4 55.0
O C OXT CA 181.2 180.2
OXT C CA N 341.4 350.2
OXT C CA CB 106.5 110.3
OXT C CA HA 223.4 230.3
N CA C OXT 341.4 350.2
C CA N CB 123.4 120.0
C CA N HA 241.9 240.0
HN N CA HNA 240.0 240.1
HN N CA H22 120.0 120.0
HNA N CA H22 240.0 239.9
CB CA N HA 118.5 120.0
N CA CB CG 314.0 295.0
N CA CB HB 74.3 55.0
N CA CB HBA 193.7 175.0
CA N HN HNA 120.0 119.9
HN N CA CB 56.6 60.0
HN N CA HA 298.1 300.0
CA N HN H22 240.0 240.0
HNA N HN H22 120.0 120.1
CA N HNA HN 240.0 240.1
HNA N CA CB 176.5 179.9
HNA N CA HA 58.1 59.9
CA N HNA H22 120.0 120.0
HN N HNA H22 240.0 239.9
C2 N1 C6 C5 357.8 359.9
C2 N1 C6 N6 178.2 180.0
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 359.1 0.0
C6 N1 C2 N3 0.3 0.0
C6 N1 C2 H2 180.3 180.0
C4 C5 C6 N1 4.6 0.1
N1 C6 C5 N7 175.5 180.1
C5 C6 N1 N6 179.6 180.0
N1 C6 N6 HN6 0.0 360.0
N1 C6 N6 HN6A 120.0 179.9
N3 C2 N1 C6 0.3 0.0
N1 C2 N3 H2 180.0 179.9
C2 N3 C4 C5 3.6 360.0
C2 N3 C4 N9 179.6 180.0
H2 C2 N1 C6 180.3 180.0
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 179.1 180.1
C4 N3 C2 H2 179.1 180.1
C5 C4 N3 N9 183.9 180.0
N3 C4 C5 C6 354.5 360.0
N3 C4 C5 N7 181.9 180.0
N3 C4 N9 C8 182.7 180.0
N3 C4 N9 C1' 355.7 359.9
N1 C6 C5 C4 4.6 0.1
N3 C4 C5 N9 176.9 180.0
C5 C4 N9 C8 359.3 0.0
C5 C4 N9 C1' 172.2 179.9
C6 C5 C4 N7 172.7 180.0
C4 C5 C6 N6 184.2 180.0
C4 C5 N7 C8 352.8 360.0
N3 C4 N9 C5 183.4 180.0
N9 C4 C5 C6 177.6 180.0
N9 C4 C5 N7 4.9 360.0
N7 C8 N9 C4 356.4 360.0
C4 N9 C8 H8 176.4 180.0
C8 N9 C4 C1' 187.0 180.1
C4 N9 C1' C2' 133.5 85.0
C4 N9 C1' O4' 247.3 199.1
C4 N9 C1' H1' 7.6 322.2
N1 C6 C5 N6 180.4 180.0
C6 C5 C4 N9 177.6 180.0
C4 C5 C6 N7 189.1 180.0
C6 C5 N7 C8 181.4 180.0
C5 C6 N6 HN6 180.5 180.0
C5 C6 N6 HN6A 300.5 360.0
N7 C5 C4 N9 4.9 360.0
C4 C5 N7 C6 171.5 180.0
N7 C5 C6 N6 355.1 0.0
C5 N7 C8 N9 6.6 0.0
C5 N7 C8 H8 186.6 180.0
N1 C6 N6 C5 179.6 180.0
N6 C6 C5 N7 355.1 0.0
HN6 N6 C6 HN6A 240.0 180.1
C6 N6 HN6 HN6A 120.0 179.9
C6 N6 HN6A HN6 240.0 180.1
C4 N9 C8 N7 356.4 360.0
N9 C8 N7 H8 180.0 180.1
N7 C8 N9 C1' 184.1 180.1
C4 N9 C8 C1' 172.3 179.9
N7 C8 N9 H8 180.0 179.9
C8 N9 C1' C2' 304.7 265.0
C8 N9 C1' O4' 58.6 19.0
C8 N9 C1' H1' 178.9 142.1
N7 C8 H8 N9 180.0 180.1
H8 C8 N9 C1' 4.1 0.1
C4 N9 C1' C8 188.8 180.1
C1' N9 C8 H8 4.1 0.1
C2' C1' N9 O4' 246.1 246.0
C2' C1' N9 H1' 125.8 122.9
N9 C1' C2' O2' 282.6 273.7
N9 C1' C2' C3' 157.5 155.5
N9 C1' C2' H2' 44.1 37.3
O4' C1' N9 H1' 239.7 236.9
N9 C1' O4' C4' 195.1 201.4
CB CA C OXT 106.5 110.3
C CA CB N 235.8 240.0
C CA CB HA 117.1 120.0
CB CA N HN 56.6 60.0
CB CA N HNA 176.5 179.9
N CA CB HA 241.4 240.0
CB CA N H22 296.6 300.0
CG CB CA HB 239.7 240.0
CG CB CA HBA 120.3 120.0
CA CB CG SD 211.3 180.0
CA CB CG HG 331.3 300.0
CA CB CG HGA 91.3 60.0
HB CB CA HBA 240.7 240.0
HA CA C OXT 223.4 230.3
C CA HA N 120.1 119.9
C CA HA CB 241.7 240.0
HA CA N HN 298.1 300.0
HA CA N HNA 58.1 59.9
N CA HA CB 121.6 120.0
HA CA N H22 178.1 180.0
HA CA CB CG 72.7 55.0
HA CA CB HB 193.0 174.9
HA CA CB HBA 312.3 294.9
CG CB CA HA 72.7 55.0
CA CB CG HB 120.3 120.0
CA CB CG HBA 239.7 239.9
HB CB CG HBA 119.3 120.0
CE SD CG CB 293.4 286.9
CB CG SD C5' 183.6 180.0
SD CG CB HG 240.0 240.0
SD CG CB HGA 120.0 120.0
HG CG CB HGA 240.0 240.0
HB CB CA HA 193.0 174.9
CA CB HB CG 238.0 240.0
CA CB HB HBA 119.0 120.0
CG CB HB HBA 241.0 240.0
HB CB CG SD 91.0 60.0
HB CB CG HG 211.0 180.0
HB CB CG HGA 331.0 300.0
HBA CB CA HA 312.3 294.9
CA CB HBA CG 122.0 120.0
CA CB HBA HB 241.0 240.0
CG CB HBA HB 119.0 119.9
HBA CB CG SD 331.7 300.0
HBA CB CG HG 91.7 60.1
HBA CB CG HGA 211.6 180.1
CB CG SD CE 293.4 286.9
CG SD CE C5' 255.4 253.1
CE SD CG HG 173.4 166.8
CE SD CG HGA 53.4 46.8
CE SD C5' C4' 180.0 61.6
CE SD C5' H5' 300.2 181.6
CE SD C5' H5'A 59.8 301.6
CZ CE SD HE 239.6 240.0
CZ CE SD HEA 120.4 120.0
SD CE CZ OZ1 168.3 6.8
SD CE CZ OZ2 2.5 186.8
HE CE SD HEA 240.8 240.0
SD CG CB HB 91.0 60.0
SD CG CB HBA 331.7 300.0
CB CG SD HG 120.0 120.0
CB CG SD HGA 240.0 240.0
CE SD CG C5' 109.8 106.9
CG SD CE CZ 172.0 303.1
CG SD CE HE 292.4 63.1
CG SD CE HEA 51.6 183.1
CG SD C5' C4' 287.2 168.5
CG SD C5' H5' 47.3 288.4
CG SD C5' H5'A 167.0 48.5
HG CG SD HGA 120.0 120.0
CE SD C5' CG 252.8 253.1
C5' SD CE CZ 276.6 50.0
C5' SD CE HE 37.0 170.0
C5' SD CE HEA 156.2 290.0
C5' SD CG HG 63.6 60.0
C5' SD CG HGA 303.6 300.0
C3' C4' C5' SD 280.4 185.2
O4' C4' C5' SD 162.9 67.3
SD C5' C4' H4' 42.8 306.2
C4' C5' SD H5' 239.8 240.0
C4' C5' SD H5'A 120.2 120.0
H5' C5' SD H5'A 240.3 240.0
CZ CE SD CG 172.0 303.1
CZ CE SD C5' 276.6 50.0
SD CE CZ HE 120.4 120.0
SD CE CZ HEA 239.6 240.0
HE CE CZ HEA 119.2 120.1
OZ1 CZ CE OZ2 165.8 180.0
HE CE SD CG 292.4 63.1
HE CE SD C5' 37.0 170.0
SD CE HE CZ 237.4 240.0
SD CE HE HEA 118.7 119.9
CZ CE HE HEA 241.3 239.9
HE CE CZ OZ1 47.9 246.8
HE CE CZ OZ2 242.1 66.8
HEA CE SD CG 51.6 183.1
HEA CE SD C5' 156.2 290.0
SD CE HEA CZ 122.6 120.0
SD CE HEA HE 241.3 240.1
CZ CE HEA HE 118.7 120.1
HEA CE CZ OZ1 288.7 126.8
HEA CE CZ OZ2 122.9 306.8
HG CG CB HB 211.0 180.0
HG CG CB HBA 91.7 60.1
CB CG HG SD 239.8 240.0
CB CG HG HGA 119.9 120.0
HG CG SD C5' 63.6 60.0
SD CG HG HGA 240.1 240.0
HGA CG CB HB 331.0 300.0
HGA CG CB HBA 211.6 180.1
CB CG HGA SD 120.2 120.0
CB CG HGA HG 240.1 240.0
HGA CG SD C5' 303.6 300.0
SD CG HGA HG 119.9 120.0
OZ1 CZ CE HE 47.9 246.8
OZ1 CZ CE HEA 288.7 126.8
CE CZ OZ1 OZ2 195.2 180.0
OZ2 CZ CE HE 242.1 66.8
OZ2 CZ CE HEA 122.9 306.8
CE CZ OZ2 OZ1 164.1 180.0
N9 C1' C2' O4' 114.6 118.5
N9 C1' C2' H1' 233.9 237.2
O4' C1' C2' H1' 119.3 118.7
C2' C1' O4' C4' 316.8 319.9
O2' C2' C1' C3' 125.1 118.2
O2' C2' C1' H2' 238.5 236.5
C1' C2' O2' HO2' 180.0 180.0
C3' C2' C1' H2' 113.5 118.3
C1' C2' C3' O3' 98.5 97.7
C1' C2' C3' C4' 334.8 339.1
C1' C2' C3' H3' 219.8 220.3
N9 C1' O4' C2' 238.3 241.6
N9 C1' O4' H1' 119.8 123.0
C2' C1' O4' H1' 241.5 241.4
O4' C1' C2' O2' 168.0 155.3
O4' C1' C2' C3' 42.9 37.1
O4' C1' C2' H2' 289.5 278.8
C3' C4' O4' C1' 26.7 26.6
C1' O4' C4' C5' 146.6 146.0
C1' O4' C4' H4' 265.8 267.1
N9 C1' H1' C2' 128.8 122.8
N9 C1' H1' O4' 243.5 237.0
C2' C1' H1' O4' 114.7 114.1
H1' C1' C2' O2' 48.7 36.6
H1' C1' C2' C3' 283.6 278.4
H1' C1' C2' H2' 170.1 160.1
H1' C1' O4' C4' 75.3 78.4
O2' C2' C1' O4' 168.0 155.3
O2' C2' C1' H1' 48.7 36.6
C1' C2' O2' C3' 243.0 247.3
C1' C2' O2' H2' 120.7 123.7
C3' C2' O2' H2' 237.8 236.4
O2' C2' C3' O3' 335.0 339.5
O2' C2' C3' C4' 211.3 220.9
O2' C2' C3' H3' 96.3 102.1
C3' C2' C1' O4' 42.9 37.1
C3' C2' C1' H1' 283.6 278.4
C1' C2' C3' O2' 123.5 118.2
C1' C2' C3' H2' 246.5 241.7
O2' C2' C3' H2' 123.0 123.5
C3' C2' O2' HO2' 297.0 292.7
O3' C3' C2' C4' 123.7 118.6
O3' C3' C2' H3' 238.7 237.4
C2' C3' O3' HO3' 180.0 61.5
C4' C3' C2' H3' 115.0 118.8
C2' C3' C4' O4' 0.2 357.9
C2' C3' C4' C5' 243.7 238.5
C2' C3' C4' H4' 121.5 117.4
H2' C2' C1' O4' 289.5 278.8
H2' C2' C1' H1' 170.1 160.1
C1' C2' H2' O2' 236.0 236.4
C1' C2' H2' C3' 109.1 112.8
O2' C2' H2' C3' 233.2 236.4
H2' C2' O2' HO2' 59.2 56.4
H2' C2' C3' O3' 212.0 216.0
H2' C2' C3' C4' 88.3 97.4
H2' C2' C3' H3' 333.3 338.6
HO2' O2' C2' C3' 297.0 292.7
HO2' O2' C2' H2' 59.2 56.4
O3' C3' C2' H2' 212.0 216.0
C2' C3' O3' C4' 242.8 245.3
C2' C3' O3' H3' 120.7 122.6
C4' C3' O3' H3' 237.9 237.3
O3' C3' C4' O4' 237.9 239.3
O3' C3' C4' C5' 121.4 119.9
O3' C3' C4' H4' 359.2 358.8
SD C5' C4' C3' 280.4 185.2
C1' O4' C4' C3' 26.7 26.6
C4' C3' C2' H2' 88.3 97.4
C2' C3' C4' O3' 122.3 118.6
C2' C3' C4' H3' 245.0 241.3
O3' C3' C4' H3' 122.7 122.7
C4' C3' O3' HO3' 297.2 176.2
O4' C4' C3' C5' 116.5 119.4
O4' C4' C3' H4' 238.7 240.5
C5' C4' C3' H4' 122.2 121.1
C3' C4' C5' H5' 160.2 65.2
C3' C4' C5' H5'A 40.6 305.1
H3' C3' C2' H2' 333.3 338.6
C2' C3' H3' O3' 237.0 237.4
C2' C3' H3' C4' 111.5 114.8
O3' C3' H3' C4' 234.5 237.3
H3' C3' O3' HO3' 59.3 299.0
H3' C3' C4' O4' 115.2 116.7
H3' C3' C4' C5' 358.7 357.2
H3' C3' C4' H4' 236.5 236.1
HO3' O3' C3' C4' 297.2 176.2
HO3' O3' C3' H3' 59.3 299.0
SD C5' C4' O4' 162.9 67.3
C4' O4' C1' H1' 75.3 78.4
O4' C4' C3' H3' 115.2 116.7
C3' C4' O4' C5' 240.0 240.6
C3' C4' O4' H4' 120.8 119.5
C5' C4' O4' H4' 240.8 238.8
O4' C4' C5' H5' 42.7 307.4
O4' C4' C5' H5'A 283.0 187.3
SD C5' C4' H5' 120.2 119.9
SD C5' C4' H5'A 239.8 240.0
C5' C4' C3' H3' 358.7 357.2
C3' C4' C5' O4' 117.5 117.8
C3' C4' C5' H4' 237.6 238.9
O4' C4' C5' H4' 120.1 121.1
H5' C5' C4' H5'A 119.6 120.1
H4' C4' C3' H3' 236.5 236.1
C3' C4' H4' O4' 240.5 242.1
C3' C4' H4' C5' 123.3 121.0
O4' C4' H4' C5' 242.8 238.9
H4' C4' C5' H5' 282.6 186.3
H4' C4' C5' H5'A 163.0 66.2
SD C5' H5' C4' 239.0 240.0
SD C5' H5' H5'A 119.5 120.0
H5' C5' C4' H4' 282.6 186.3
C4' C5' H5' H5'A 240.5 239.9
SD C5' H5'A C4' 121.0 120.0
SD C5' H5'A H5' 240.5 240.0
H5'A C5' C4' H4' 163.0 66.2
C4' C5' H5'A H5' 119.5 120.0
CA N H22 HN 120.0 120.0
CA N H22 HNA 240.0 239.9
H22 N CA CB 296.6 300.0
H22 N CA HA 178.1 180.0
HN N H22 HNA 120.0 120.0