Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UDP

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 39


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -3.586 0.41 0.193
2 C2 C C2 N N N 0 -4.585 0.798 1.007
3 N3 N N3 N N N 0 -5.335 1.877 0.717
4 C4 C C4 N N N 0 -5.094 2.591 -0.401
5 C5 C C5 N N N 0 -4.045 2.195 -1.266
6 C6 C C6 N N N 0 -3.309 1.107 -0.951
7 O2 O O2 N N N 0 -4.815 0.163 2.019
8 O4 O O4 N N N 0 -5.771 3.568 -0.665
9 C1' C C1' R N N 0 -2.784 -0.766 0.539
10 C2' C C2' R N N 0 -2.99 -1.893 -0.505
11 O2' O O2' N N N 0 -4.127 -2.694 -0.174
12 C3' C C3' S N N 0 -1.681 -2.708 -0.366
13 C4' C C4' R N N 0 -0.691 -1.722 0.283
14 O4' O O4' N N N 0 -1.375 -0.468 0.438
15 O3' O O3' N N N 0 -1.885 -3.842 0.479
16 C5' C C5' N N N 0 0.53 -1.54 -0.621
17 O5' O O5' N N N 0 1.494 -0.718 0.04
18 PA P PA N N N 0 2.907 -0.318 -0.621
19 O1A O O1A N N N 0 3.63 -1.546 -1.019
20 O2A O O2A N N N 0 2.651 0.599 -1.92
21 O3A O O3A N N N 0 3.787 0.501 0.449
22 PB P PB N N N 0 5.343 0.907 0.541
23 O1B O O1B N N N 0 6.176 -0.227 0.081
24 O2B O O2B N N Y 0 5.619 2.189 -0.393
25 O3B O O3B N N N 0 5.716 1.263 2.066
26 HN3 H HN3 N N N 0 -6.052 2.143 1.314
27 H5 H H5 N N N 0 -3.837 2.754 -2.166
28 H6 H H6 N N N 0 -2.506 0.79 -1.599
29 H1' H H1' N N N 0 -3.034 -1.119 1.539
30 H2' H H2' N N N 0 -3.087 -1.48 -1.51
31 HO2' H HO2' N N N 0 -4.297 -3.412 -0.798
32 H3' H H3' N N N 0 -1.321 -3.021 -1.346
33 H4' H H4' N N N 0 -0.38 -2.098 1.258
34 HO3' H HO3' N N N 0 -2.544 -4.467 0.146
35 H5'1 H H5'1 N N N 0 0.97 -2.514 -0.837
36 H5'2 H H5'2 N N N 0 0.225 -1.064 -1.553
37 HOA2 H HOA2 N N N 0 2.179 1.422 -1.733
38 HOB2 H HOB2 N N N 0 5.105 2.971 -0.148
39 HOB3 H HOB3 N N N 0 6.64 1.517 2.196