Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : C5G

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 61


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -5.978 0.775 0.705
2 C2 C C2 N Y N 0 -5.765 1.504 -0.405
3 N3 N N3 N Y N 0 -6.35 2.689 -0.573
4 C4 C C4 N Y N 0 -7.161 3.181 0.355
5 C5 C C5 N Y N 0 -7.4 2.444 1.533
6 C6 C C6 N Y N 0 -6.802 1.239 1.686
7 O2 O O2 N N N 0 -5.023 1.073 -1.273
8 N4 N N4 N N N 0 -7.759 4.406 0.171
9 C1D C C1* R N N 0 -5.32 -0.524 0.861
10 C2D C C2* R N N 0 -5.801 -1.505 -0.231
11 O2D O O2* N N N 0 -6.82 -2.369 0.276
12 C3D C C3* S N N 0 -4.533 -2.316 -0.591
13 C4D C C4* R N N 0 -3.439 -1.73 0.33
14 O4D O O4* N N N 0 -3.897 -0.397 0.645
15 O3D O O3* N N N 0 -4.73 -3.704 -0.314
16 C5D C C5* N N N 0 -2.098 -1.672 -0.403
17 O5D O O5* N N N 0 -1.093 -1.169 0.48
18 PA P PA R N N 0 0.284 -1.136 -0.353
19 O1A O O1A N N N 0 0.558 -2.481 -0.907
20 O2A O O2A N N N 0 0.158 -0.075 -1.556
21 O3A O O3A N N N 0 1.49 -0.702 0.622
22 PB P PB R N N 0 2.86 -1.069 -0.14
23 O1B O O1B N N N 0 2.772 -0.631 -1.551
24 O2B O O2B N N N 0 3.094 -2.66 -0.086
25 O1' O O1' N N N 0 4.091 -0.32 0.578
26 C1' C C1' R N N 0 5.253 -0.587 -0.209
27 C2' C C2' R N N 0 6.488 -0.599 0.694
28 O2' O O2' N N N 0 6.354 -1.632 1.673
29 C3' C C3' S N N 0 6.609 0.757 1.395
30 O3' O O3' N N N 0 7.836 0.816 2.125
31 C4' C C4' S N N 0 6.591 1.861 0.331
32 O4' O O4' N N N 0 6.554 3.14 0.966
33 C5' C C5' R N N 0 5.349 1.688 -0.546
34 C6' C C6' N N N 0 5.305 2.805 -1.59
35 O6' O O6' N N N 0 4.085 2.719 -2.33
36 O5' O O5' N N N 0 5.394 0.424 -1.205
37 H5 H H5 N N N 0 -8.058 2.831 2.297
38 H6 H H6 N N N 0 -6.974 0.654 2.577
39 H41 H 1H4 N N N 0 -7.589 4.912 -0.639
40 H42 H 2H4 N N N 0 -8.354 4.762 0.849
41 H1D H H1* N N N 0 -5.518 -0.933 1.852
42 H2D H H2* N N N 0 -6.164 -0.958 -1.101
43 HO'2 H 2HO* N N N 0 -7.034 -2.994 -0.43
44 H3D H H3* N N N 0 -4.269 -2.17 -1.638
45 H4D H H4* N N N 0 -3.349 -2.325 1.238
46 H3T H H3T N N N 0 -5.421 -4.013 -0.916
47 H5'1 H 1H5* N N N 0 -1.822 -2.673 -0.735
48 H5'2 H 2H5* N N N 0 -2.184 -1.014 -1.268
49 HO2A H HO2A N N N 0 -0.02 0.786 -1.153
50 HO2B H HO2B N N N 0 3.146 -2.904 0.848
51 H1' H H1' N N N 0 5.148 -1.559 -0.692
52 H2' H H2' N N N 0 7.379 -0.78 0.093
53 HOD H 2HO' N N N 0 6.281 -2.467 1.19
54 H3' H H3' N N N 0 5.77 0.894 2.077
55 HO'3 H 3HO' N N N 0 7.804 0.107 2.782
56 H4' H H4' N N N 0 7.486 1.786 -0.287
57 HO'4 H 4HO' N N N 0 7.353 3.207 1.507
58 H5' H H5' N N N 0 4.456 1.74 0.077
59 H6'1 H 1H6' N N N 0 5.36 3.772 -1.091
60 H6'2 H 2H6' N N N 0 6.151 2.699 -2.271
61 HO'6 H 6HO' N N N 0 4.098 3.439 -2.975