Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : AKM

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 65


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 4.863 -0.176 -0.212
2 C1' C C1* R N N 0 -5.256 0.019 -1.356
3 C2 C C2 N N N 0 5.337 -1.019 -1.396
4 C2' C C2* N N N 0 -6.076 1.323 -1.391
5 C21 C C21 N N N 0 -6.126 -0.78 0.768
6 C3 C C3 S N N 0 6.829 -1.313 -1.27
7 C3' C C3* S N N 0 -5.117 2.389 -0.807
8 C3M C C3M N N N 0 7.643 -0.05 -1.562
9 C4 C C4 N N N 0 7.183 -1.882 0.098
10 C4' C C4* R N N 0 -3.731 1.727 -1.013
11 C41 C C41 N N N 0 -7.239 -2.823 0.986
12 C5 C C5 R N N 0 6.473 -1.21 1.262
13 C5' C C5* N N N 0 -2.716 2.28 -0.01
14 C51 C C51 N N N 0 -7.063 -3.053 -0.4
15 C5A C C5A N N N 0 -7.585 -4.315 -1.037
16 C6 C C6 N N N 0 7.237 0.027 1.736
17 C61 C C61 N N N 0 -6.426 -2.124 -1.145
18 H1 H H1 N N N 0 -0.549 0.596 2.272
19 H11 H H11 N N N 0 7.099 -3.734 0.933
20 H12 H H12 N N N 0 8.916 -2.098 1.142
21 H13 H H13 N N N 0 6.476 -1.929 2.109
22 H14 H H14 N N N 0 6.778 0.411 2.647
23 H15 H H15 N N N 0 8.274 -0.241 1.937
24 H16 H H16 N N N 0 7.204 0.794 0.961
25 H17 H H17 N N N 0 3.085 2.637 -1.506
26 H18 H H18 N N N 0 -3.054 2.066 1.004
27 H19 H H19 N N N 0 -2.624 3.358 -0.143
28 H2 H H2 N N N 0 5.373 0.784 -0.203
29 H20 H H20 N N N 0 -3.38 1.875 -2.034
30 H21 H H21 N N N 0 -5.317 2.553 0.252
31 H22 H H22 N N N 0 -6.06 4.066 -1.44
32 H23 H H23 N N N 0 -6.967 1.23 -0.77
33 H24 H H24 N N N 0 -6.348 1.575 -2.416
34 H25 H H25 N N N 0 -5.111 -0.355 -2.37
35 H26 H H26 N N N 0 -6.879 -1.521 2.482
36 H27 H H27 N N N 0 -8.069 -4.931 -0.278
37 H28 H H28 N N N 0 -8.308 -4.059 -1.812
38 H29 H H29 N N N 0 -6.757 -4.868 -1.48
39 H3 H H3 N N N 0 4.779 -1.957 -1.418
40 H30 H H30 N N N 0 -6.286 -2.28 -2.204
41 H4 H H4 N N N 0 5.149 -0.475 -2.325
42 H5 H H5 N N N 0 7.371 0.73 -0.851
43 H6 H H6 N N N 0 8.706 -0.272 -1.469
44 H7 H H7 N N N 0 7.431 0.292 -2.575
45 H8 H H8 N N N 0 6.986 -1.982 -3.223
46 H9 H H9 N N N 0 8.151 -2.6 -2.21
47 N11 N N11 N N N 0 -5.953 -0.986 -0.55
48 N3 N N3 N N N 0 7.184 -2.323 -2.294
49 N31 N N31 N N N 0 -6.762 -1.686 1.533
50 O1 O O1 N N N 0 3.453 0.052 -0.334
51 O1P O O1P N N N 0 0.109 3.466 0.61
52 O21 O O21 N N N 0 -5.702 0.241 1.276
53 O2P O O2P N N N 0 -0.38 1.543 2.171
54 O3' O O3* N N N 0 -5.211 3.614 -1.537
55 O3P O O3P N N N 0 3.033 1.513 1.681
56 O4' O O4* N N N 0 -3.985 0.328 -0.761
57 O41 O O41 N N N 0 -7.815 -3.643 1.677
58 O4A O O4A N N N 0 6.865 -3.285 0.109
59 O4B O O4B N N N 0 8.604 -1.758 0.292
60 O4P O O4P N N N 0 3.253 2.664 -0.555
61 O5 O O5 N N N 0 5.119 -0.893 0.991
62 O5' O O5* N N N 0 -1.446 1.663 -0.229
63 OPP O OPP N N N 0 1.133 1.229 0.044
64 P P P N N N 0 -0.14 2.007 0.648
65 P2 P P2 N N N 0 2.725 1.368 0.241