Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UD4

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 66


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N3 N N3 N N N 0 -6.747 -2.999 -0.873
2 C2 C C2 N N N 0 -6.271 -1.808 -1.279
3 N1 N N1 N N N 0 -5.643 -0.985 -0.42
4 C4 C C4 N N N 0 -6.606 -3.385 0.412
5 C5 C C5 N N N 0 -5.946 -2.529 1.326
6 C6 C C6 N N N 0 -5.473 -1.342 0.89
7 O7' O O7' N N N 0 7.161 1.208 -1.675
8 C7' C C7' N N N 0 6.166 1.044 -2.35
9 C8' C C8' N N N 0 5.894 1.95 -3.524
10 N2' N N2' N N N 0 5.305 0.052 -2.051
11 C2' C C2' R N N 0 5.569 -0.828 -0.91
12 C3' C C3' S N N 0 4.869 -2.173 -1.128
13 O3' O O3' N N N 0 5.417 -2.816 -2.28
14 C4' C C4' S N N 0 5.087 -3.056 0.105
15 N4A N N4A N N N 0 4.358 -4.32 -0.062
16 C5' C C5' R N N 0 4.568 -2.325 1.345
17 C6' C C6' N N N 0 4.837 -3.174 2.589
18 O5' O O5' N N N 0 5.238 -1.069 1.472
19 C1' C C1' R N N 0 5.031 -0.183 0.37
20 O1' O O1' N N N 0 3.633 0.075 0.222
21 PB P PB R N N 0 2.883 1.293 0.961
22 O2B O O2B N N N 0 3.125 1.209 2.419
23 O1B O O1B N N N 0 3.451 2.692 0.402
24 O3A O O3A N N N 0 1.301 1.203 0.674
25 PA P PA R N N 0 0.004 1.89 1.334
26 O2A O O2A N N N 0 -0.307 1.198 2.753
27 O1A O O1A N N N 0 0.259 3.334 1.535
28 O5B O O5B N N N 0 -1.261 1.7 0.356
29 C5B C C5B N N N 0 -2.538 2.288 0.611
30 C4B C C4B R N N 0 -3.507 1.909 -0.511
31 O4B O O4B N N N 0 -3.764 0.495 -0.477
32 C2B C C2B S N N 0 -4.856 2.625 -0.302
33 O3B O O3B N N N 0 -5.153 3.467 -1.418
34 C3B C C3B R N N 0 -5.885 1.473 -0.203
35 O4 O O4 N N N 0 -7.041 -4.461 0.781
36 O2' O O2' N N N 0 -7.083 1.798 -0.911
37 C1B C C1B R N N 0 -5.134 0.306 -0.892
38 O2 O O2 N N N 0 -6.411 -1.47 -2.439
39 H5 H H5 N N N 0 -5.824 -2.821 2.358
40 H6 H H6 N N N 0 -4.968 -0.676 1.573
41 H8' H H8' N N N 0 6.695 2.685 -3.608
42 H8'A H H8'A N N N 0 5.848 1.357 -4.437
43 H8'B H H8'B N N N 0 4.944 2.463 -3.374
44 HN2' H HN2' N N N 0 4.509 -0.079 -2.59
45 H2' H H2' N N N 0 6.643 -0.988 -0.814
46 H3' H H3' N N N 0 3.801 -2.009 -1.274
47 HO3' H HO3' N N N 0 5.019 -3.675 -2.478
48 H4' H H4' N N N 0 6.151 -3.262 0.221
49 HN4A H HN4A N N N 0 4.487 -4.92 0.74
50 HN4B H HN4B N N N 0 3.378 -4.152 -0.234
51 H5' H H5' N N N 0 3.496 -2.156 1.245
52 H6' H H6' N N N 0 5.909 -3.342 2.689
53 H6'A H H6'A N N N 0 4.467 -2.654 3.472
54 H6'B H H6'B N N N 0 4.326 -4.133 2.491
55 H1' H H1' N N N 0 5.556 0.754 0.553
56 HO1B H HO1B N N N 0 3.327 2.815 -0.549
57 HO2A H HO2A N N N 0 -0.484 0.249 2.698
58 H5B H H5B N N N 0 -2.922 1.923 1.563
59 H5BA H H5BA N N N 0 -2.436 3.373 0.652
60 H4B H H4B N N N 0 -3.083 2.185 -1.476
61 H2B H H2B N N N 0 -4.84 3.206 0.62
62 HO3B H HO3B N N N 0 -5.991 3.943 -1.339
63 H3B H H3B N N N 0 -6.103 1.235 0.838
64 HO2' H HO2' N N N 0 -7.542 2.579 -0.572
65 H1B H H1B N N N 0 -5.223 0.379 -1.976
66 HN3 H HN3 N N N 0 -7.198 -3.58 -1.505