Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UGB

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 59


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 5.66 -1.138 0.278
2 C2 C C2 N N N 0 6.22 -2.107 1.025
3 O2 O O2 N N N 0 6.269 -1.98 2.233
4 N3 N N3 N N N 0 6.724 -3.217 0.453
5 C4 C C4 N N N 0 6.676 -3.373 -0.885
6 O4 O O4 N N N 0 7.132 -4.377 -1.403
7 C5 C C5 N N N 0 6.091 -2.361 -1.683
8 C6 C C6 N N N 0 5.592 -1.258 -1.083
9 PA P PA N N N 0 0.059 1.973 -1.239
10 PB P PB N N N 0 -2.832 1.335 -1.09
11 O'P O O'P N N N 0 -6.625 -2.539 -1.777
12 O'Q O O'Q N N N 0 -5.51 -4.081 -0.653
13 C1' C C1' R N N 0 -5.124 0.69 0.122
14 O1A O O1A N N N 0 0.434 1.509 -2.735
15 O1B O O1B N N N 0 -3.144 0.608 -2.492
16 C1D C C1D R N N 0 5.114 0.056 0.929
17 C2' C C2' R N N 0 -5.592 0.649 1.579
18 O2' O O2' N N N 0 -5.011 1.738 2.298
19 O2A O O2A N N N 0 -0.192 3.431 -1.224
20 O2B O O2B N N N 0 -3.19 2.768 -1.186
21 C2D C C2D R N N 0 5.882 1.324 0.477
22 O2D O O2D N N N 0 7.041 1.534 1.286
23 C3' C C3' S N N 0 -5.152 -0.675 2.211
24 O3' O O3' N N N 0 -5.647 -0.754 3.549
25 O3A O O3A N N N 0 -1.264 1.196 -0.751
26 O3B O O3B N N N 0 -3.697 0.643 0.078
27 C3D C C3D S N N 0 4.834 2.439 0.713
28 O3D O O3D N N N 0 5.068 3.088 1.964
29 C4' C C4' R N N 0 -5.716 -1.835 1.386
30 O4' O O4' N N N 0 -7.144 -1.8 1.428
31 C4D C C4D R N N 0 3.486 1.691 0.737
32 O4D O O4D N N N 0 3.761 0.301 0.488
33 C5' C C5' S N N 0 -5.244 -1.698 -0.063
34 O5' O O5' N N N 0 -5.66 -0.433 -0.581
35 C5D C C5D N N N 0 2.565 2.244 -0.353
36 O5D O O5D N N N 0 1.28 1.628 -0.248
37 C6' C C6' N N N 0 -5.844 -2.803 -0.894
38 H5 H H5 N N N 0 6.043 -2.468 -2.756
39 H6 H H6 N N N 0 5.141 -0.476 -1.675
40 HO'Q H HO'Q N N N 0 -5.92 -4.754 -1.212
41 H1' H H1' N N N 0 -5.472 1.611 -0.346
42 HO1A H HO1A N N N 0 0.611 0.562 -2.82
43 HO1B H HO1B N N N 0 -2.933 -0.336 -2.502
44 H1D H H1D N N N 0 5.151 -0.049 2.013
45 H2' H H2' N N N 0 -6.679 0.727 1.615
46 HO2' H HO2' N N N 0 -5.244 2.609 1.948
47 H2D H H2D N N N 0 6.152 1.26 -0.577
48 HO2D H HO2D N N N 0 7.554 2.316 1.041
49 H3' H H3' N N N 0 -4.063 -0.729 2.222
50 HO3' H HO3' N N N 0 -5.334 -0.044 4.127
51 H3D H H3D N N N 0 4.857 3.162 -0.102
52 HO3D H HO3D N N N 0 5.928 3.526 2.025
53 H4' H H4' N N N 0 -5.363 -2.781 1.798
54 HO4' H HO4' N N N 0 -7.57 -2.508 0.926
55 H4D H H4D N N N 0 3.017 1.804 1.714
56 H5' H H5' N N N 0 -4.156 -1.765 -0.099
57 H5D H H5D N N N 0 2.462 3.322 -0.229
58 H5DA H H5DA N N N 0 2.993 2.03 -1.332
59 HN3 H HN3 N N N 0 7.124 -3.906 1.007