Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : CDC

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 57


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 5.094 -0.536 0.567
2 C2 C C2 N N N 0 4.718 -1.312 -0.467
3 N3 N N3 N N N 0 5.308 -2.484 -0.697
4 C4 C C4 N N N 0 6.276 -2.922 0.097
5 C5 C C5 N N N 0 6.689 -2.136 1.192
6 C6 C C6 N N N 0 6.084 -0.944 1.409
7 O2 O O2 N N N 0 3.831 -0.93 -1.212
8 N4 N N4 N N N 0 6.874 -4.137 -0.148
9 C1' C C1* R N N 0 4.431 0.751 0.79
10 C2' C C2* R N N 0 4.629 1.69 -0.427
11 O2' O O2* N N N 0 5.856 2.414 -0.318
12 C3' C C3* S N N 0 3.411 2.643 -0.303
13 C4' C C4* R N N 0 2.41 1.86 0.568
14 O4' O O4* N N N 0 2.998 0.58 0.855
15 O3' O O3* N N N 0 3.794 3.863 0.336
16 C5' C C5* N N N 0 1.096 1.67 -0.192
17 O5' O O5* N N N 0 0.139 1.041 0.661
18 PA P PA S N N 0 -1.212 0.873 -0.199
19 O1A O O1A N N N 0 -0.913 0.139 -1.449
20 O2A O O2A N N N 0 -1.803 2.326 -0.558
21 O3A O O3A N N N 0 -2.297 0.05 0.66
22 PB P PB N N N 0 -3.37 -0.538 -0.386
23 O1B O O1B N N N 0 -4.73 -0.908 0.392
24 O2B O O2B N N N -1 -3.668 0.523 -1.468
25 O3B O O3B N N N 0 -2.797 -1.808 -1.053
26 C14 C C14 N N N 0 -5.677 -1.31 -0.6
27 C15 C C15 N N N 0 -6.999 -1.677 0.076
28 N11 N N11 N N N 1 -7.609 -0.469 0.649
29 C16 C C16 N N N 0 -7.755 0.549 -0.399
30 C17 C C17 N N N 0 -6.749 0.051 1.721
31 C18 C C18 N N N 0 -8.93 -0.801 1.198
32 H5 H H5 N N N 0 7.476 -2.479 1.847
33 H6 H H6 N N N 0 6.382 -0.324 2.242
34 H41 H 1H4 N N N 0 7.582 -4.454 0.434
35 H42 H 2H4 N N N 0 6.588 -4.675 -0.902
36 H1' H H1* N N N 0 4.803 1.22 1.701
37 H2' H H2* N N N 0 4.592 1.129 -1.361
38 HO'2 H 2HO* N N N 0 5.919 2.977 -1.102
39 H3' H H3* N N N 0 2.984 2.846 -1.285
40 H4' H H4* N N N 0 2.226 2.4 1.497
41 H3T H H3T N N N 0 4.464 4.275 -0.226
42 H5'1 H 1H5* N N N 0 1.27 1.044 -1.067
43 H5'2 H 2H5* N N N 0 0.717 2.642 -0.51
44 HO2A H HO2A N N N 0 -1.984 2.77 0.281
45 H141 H 1H14 N N N 0 -5.292 -2.175 -1.14
46 H142 H 2H14 N N N 0 -5.842 -0.489 -1.298
47 H151 H 1H15 N N N 0 -6.813 -2.401 0.869
48 H152 H 2H15 N N N 0 -7.676 -2.111 -0.66
49 H161 H 1H16 N N N 0 -6.775 0.795 -0.807
50 H162 H 2H16 N N N 0 -8.393 0.163 -1.195
51 H163 H 3H16 N N N 0 -8.207 1.445 0.026
52 H171 H 1H17 N N N 0 -7.279 0.835 2.262
53 H172 H 2H17 N N N 0 -6.495 -0.756 2.407
54 H173 H 3H17 N N N 0 -5.837 0.461 1.288
55 H181 H 1H18 N N N 0 -9.568 -1.187 0.403
56 H182 H 2H18 N N N 0 -8.821 -1.557 1.976
57 H183 H 3H18 N N N 0 -9.382 0.095 1.623