Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : GPL

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 59


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P S N N 0 -2.195 2.799 -0.642
2 O1P O O1P N N N 0 -2.864 1.977 -1.712
3 O2P O O2P N N N 0 -3.288 3.538 0.307
4 O5' O O5* N N N 0 -1.405 1.865 0.43
5 C5' C C5* N N N 0 -0.881 2.428 1.621
6 C4' C C4* R N N 0 -0.199 1.333 2.429
7 O4' O O4* N N N 0 0.895 0.803 1.646
8 C3' C C3* S N N 0 0.409 1.846 3.73
9 O3' O O3* N N N 0 0.47 0.769 4.665
10 C2' C C2* R N N 0 1.814 2.225 3.303
11 O2' O O2* N N N 0 2.731 2.249 4.377
12 C1' C C1* R N N 0 2.135 1.12 2.308
13 N9 N N9 N Y N 0 3.143 1.487 1.316
14 C8 C C8 N Y N 0 3.085 2.565 0.464
15 N7 N N7 N Y N 0 4.141 2.642 -0.322
16 C5 C C5 N Y N 0 4.902 1.571 0.044
17 C6 C C6 N N N 0 6.173 1.152 -0.478
18 O6 O O6 N N N 0 6.769 1.739 -1.372
19 N1 N N1 N N N 0 6.621 -0.005 0.173
20 C2 C C2 N N N 0 5.93 -0.682 1.206
21 N2 N N2 N N N 0 6.557 -1.796 1.7
22 N3 N N3 N N N 0 4.766 -0.275 1.665
23 C4 C C4 N Y N 0 4.316 0.841 1.05
24 N N N N N N 0 3.498 4.366 -6.005
25 CA C CA S N N 0 3.817 5.285 -4.943
26 CB C CB N N N 0 2.599 5.63 -4.083
27 CG C CG N N N 0 1.904 4.42 -3.445
28 CD C CD N N N 0 0.659 4.796 -2.635
29 CE C CE N N N 0 0.004 3.593 -1.953
30 NZ N NZ N N N 0 -1.155 3.981 -1.159
31 C C C N N N 0 4.881 4.614 -4.097
32 O O O N N N 0 5.283 3.467 -4.246
33 OXT O OXT N N Y 0 5.319 5.424 -3.097
34 HOP2 H 2HOP N N N 0 -4.238 3.324 0.184
35 H5'1 H 1H5* N N N 0 -0.165 3.211 1.355
36 H5'2 H 2H5* N N N 0 -1.702 2.873 2.192
37 H4' H H4* N N N 0 -0.908 0.517 2.602
38 H3' H H3* N N N 0 -0.145 2.663 4.199
39 HO3' H *HO3 N N N 0 -0.447 0.539 4.878
40 H2' H H2* N N N 0 1.812 3.206 2.815
41 HO2' H *HO2 N N N 0 2.967 1.326 4.577
42 H1' H H1* N N N 0 2.521 0.216 2.791
43 H8 H H8 N N N 0 2.25 3.253 0.465
44 HN1 H HN1 N N N 0 7.515 -0.39 -0.12
45 HN21 H 1HN2 N N N 0 6.493 -2.641 1.181
46 HN22 H 2HN2 N N N 0 7.051 -1.717 2.558
47 H H 1HN N N N 0 4.166 4.222 -6.744
48 H2 H 2HN N N Y 0 2.551 4.041 -6.103
49 HA H HA N N N 0 4.248 6.169 -5.423
50 HB2 H 1HB N N N 0 2.903 6.312 -3.278
51 HB3 H 2HB N N N 0 1.869 6.183 -4.687
52 HG2 H 1HG N N N 0 2.626 3.928 -2.78
53 HG3 H 2HG N N N 0 1.647 3.69 -4.221
54 HD2 H 1HD N N N 0 -0.078 5.289 -3.281
55 HD3 H 2HD N N N 0 0.937 5.522 -1.862
56 HE2 H 1HE N N N 0 -0.303 2.857 -2.704
57 HE3 H 2HE N N N 0 0.738 3.107 -1.299
58 HZ H HNZ N N N 0 -0.845 4.638 -0.444
59 HXT H HXT N N Y 0 5.985 5.025 -2.497