Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : GDP

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 43


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 1.952 0.935 0.329
2 C2 C C2 N N N 0 6.171 -0.441 0.927
3 C2' C C2' R N N 0 2.091 2.098 -0.686
4 C3' C C3' S N N 0 0.82 2.933 -0.399
5 C4 C C4 N Y N 0 4.003 -0.529 0.133
6 C4' C C4' R N N 0 -0.133 1.943 0.299
7 C5 C C5 N Y N 0 4.272 -1.746 -0.504
8 C5' C C5' N N N 0 -1.434 1.823 -0.497
9 C6 C C6 N N N 0 5.571 -2.295 -0.396
10 C8 C C8 N Y N 0 2.2 -1.252 -0.908
11 H1' H H1' N N N 0 2.295 1.244 1.316
12 H2' H H2' N N N 0 2.088 1.724 -1.71
13 H3' H H3' N N N 0 0.38 3.294 -1.329
14 H4' H H4' N N N 0 -0.349 2.285 1.312
15 H5' H H5'1 N N N 0 -1.222 1.39 -1.475
16 H5'' H H5'2 N N N 0 -1.874 2.811 -0.625
17 H8 H H8 N N N 0 1.19 -1.31 -1.285
18 HN1 H HN1 N N N 0 7.392 -1.977 0.412
19 HN21 H HN21 N N N 0 8.023 -0.15 1.728
20 HN22 H HN22 N N N 0 6.915 1.062 2.086
21 HO2' H HO2' N N N 0 3.357 3.652 -0.979
22 HO3' H HO3' N N Y 0 1.722 4.683 0.078
23 HOA2 H HOA2 N N N 0 -4.818 2.404 0.474
24 HOB2 H HOB2 N N N 0 -7.033 -2.508 1.908
25 HOB3 H HOB3 N N N 0 -4.521 -3.259 0.151
26 N1 N N1 N N N 0 6.495 -1.62 0.324
27 N2 N N2 N N N 0 7.13 0.222 1.651
28 N3 N N3 N N N 0 4.968 0.079 0.834
29 N7 N N7 N Y N 0 3.131 -2.134 -1.125
30 N9 N N9 N Y N 0 2.691 -0.243 -0.132
31 O1A O O1A N N N 0 -3.718 0.063 -1.702
32 O1B O O1B N N N 0 -6.829 -0.831 -0.3
33 O2' O O2' N N N 0 3.271 2.861 -0.428
34 O2A O O2A N N N 0 -4.708 1.976 -0.386
35 O2B O O2B N N N 0 -6.293 -1.885 1.93
36 O3' O O3' N N N 0 1.125 4.028 0.467
37 O3A O O3A N N N 0 -4.519 -0.438 0.638
38 O3B O O3B N N N 0 -5.234 -2.787 -0.301
39 O4' O O4' N N N 0 0.533 0.67 0.344
40 O5' O O5' N N N 0 -2.348 0.981 0.208
41 O6 O O6 N N N 0 5.85 -3.35 -0.939
42 PA P PA N N N 0 -3.821 0.633 -0.34
43 PB P PB N N N 0 -5.743 -1.471 0.475