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