Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UDX

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 56


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 -0.186 -0.59 5.37
2 C2' C C2' R N N 0 -0.246 0.226 6.663
3 O2' O O2' N N N 0 -1.366 1.113 6.616
4 C3' C C3' S N N 0 1.047 1.037 6.804
5 O3' O O3' N N N 0 1.068 1.689 8.075
6 C4' C C4' R N N 0 2.239 0.081 6.688
7 O4' O O4' N N N 0 3.454 0.832 6.665
8 C5' C C5' N N N 0 2.111 -0.725 5.394
9 O5' O O5' N N N 0 0.912 -1.497 5.423
10 PB P PB S N N 0 -0.739 -0.407 2.999
11 O1B O O1B N N N 0 -2.174 -0.611 3.299
12 O2B O O2B N N N 0 -0.044 -1.83 2.707
13 O3B O O3B N N N 0 -0.021 0.292 4.259
14 O3A O O3A N N N 0 -0.591 0.537 1.704
15 PA P PA R N N 0 -1.327 -0.219 0.488
16 O1A O O1A N N N 0 -2.752 -0.426 0.827
17 O2A O O2A N N N 0 -0.622 -1.645 0.239
18 O5D O O5* N N N 0 -1.217 0.674 -0.845
19 C5D C C5* N N N 0 -1.885 -0.046 -1.882
20 C4D C C4* R N N 0 -1.816 0.752 -3.185
21 O4D O O4* N N N 0 -0.446 0.925 -3.581
22 C3D C C3* S N N 0 -2.528 -0.02 -4.312
23 O3D O O3* N N N 0 -3.617 0.739 -4.839
24 C2D C C2* R N N 0 -1.428 -0.213 -5.389
25 O2D O O2* N N N 0 -1.959 -0.012 -6.7
26 C1D C C1* R N N 0 -0.418 0.904 -5.024
27 N1 N N1 N N N 0 0.923 0.569 -5.509
28 C6 C C6 N N N 0 1.584 1.443 -6.329
29 C2 C C2 N N N 0 1.495 -0.59 -5.14
30 O2 O O2 N N N 0 0.889 -1.352 -4.411
31 N3 N N3 N N N 0 2.724 -0.924 -5.575
32 C4 C C4 N N N 0 3.409 -0.091 -6.384
33 O4 O O4 N N N 0 4.523 -0.39 -6.774
34 C5 C C5 N N N 0 2.82 1.135 -6.776
35 H1' H H1' N N N 0 -1.114 -1.151 5.253
36 H2'1 H 1H2' N N N 0 -0.348 -0.445 7.515
37 HO'2 H 2HO' N N N 0 -2.155 0.562 6.522
38 H3'1 H 1H3' N N N 0 1.1 1.782 6.01
39 HO'3 H 3HO' N N N 0 1.897 2.185 8.121
40 H4'1 H 1H4' N N N 0 2.246 -0.597 7.542
41 HO'4 H 4HO' N N N 0 4.177 0.194 6.589
42 H5'1 H 1H5' N N N 0 2.082 -0.043 4.544
43 H5'2 H 2H5' N N N 0 2.968 -1.39 5.295
44 HOB2 H 2HOB N N N 0 0.886 -1.652 2.516
45 HOA2 H 2HOA N N N 0 0.302 -1.465 0.021
46 H5A1 H 1H5* N N N 0 -1.4 -1.012 -2.023
47 H5A2 H 2H5* N N N 0 -2.928 -0.199 -1.604
48 H4A1 H 1H4* N N N 0 -2.288 1.725 -3.048
49 H3A1 H 1H3* N N N 0 -2.879 -0.986 -3.948
50 HOA3 H 3HO* N N N 0 -3.981 0.231 -5.577
51 H2A1 H 1H2* N N N 0 -0.967 -1.197 -5.304
52 HOC2 H 2HO* N N N 0 -2.577 -0.737 -6.865
53 H1'1 H 1H1* N N N 0 -0.743 1.862 -5.429
54 H61 H 1H6 N N N 0 1.119 2.374 -6.618
55 HN3 H HN3 N N N 0 3.12 -1.767 -5.302
56 H51 H 1H5 N N N 0 3.353 1.815 -7.424