Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : JK5

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 N01 N N01 N Y N 0 -5.797 0.572 -1.038
2 C02 C C02 N Y N 0 -6.837 1.391 -1.026
3 N02 N N02 N N N 0 -7.929 1.129 -1.845
4 C03 C C03 N Y N 0 -6.846 2.512 -0.202
5 C04 C C04 N Y N 0 -5.752 2.76 0.607
6 C05 C C05 N Y N 0 -4.682 1.876 0.566
7 C06 C C06 N Y N 0 -4.74 0.783 -0.276
8 C07 C C07 N N N 0 -5.722 3.964 1.514
9 C08 C C08 N N N 0 -3.582 -0.18 -0.326
10 O09 O O09 N N N 0 -1.732 -1.947 -0.584
11 N1' N N1' N N N 0 -4.105 -3.096 1.826
12 C10 C C10 N N N 0 -0.825 -2.759 -1.333
13 C11 C C11 N N N 0 0.425 -1.946 -1.674
14 N12 N N12 N N N 0 1.14 -1.604 -0.437
15 C13 C C13 N N N 0 2.348 -0.821 -0.727
16 C14 C C14 N N N 0 3.064 -0.486 0.583
17 F15 F F15 N N N 0 2.211 0.26 1.403
18 F16 F F16 N N N 0 3.421 -1.67 1.237
19 C2' C C2' N N N 0 -2.782 -3.276 1.174
20 C21 C C21 N Y N 0 4.304 0.318 0.286
21 C22 C C22 N Y N 0 4.238 1.697 0.238
22 C23 C C23 N Y N 0 5.377 2.436 -0.036
23 F23 F F23 N N N 0 5.313 3.784 -0.083
24 C24 C C24 N Y N 0 6.582 1.791 -0.259
25 C25 C C25 N Y N 0 6.646 0.41 -0.21
26 CL25 CL CL25 N N N 0 8.156 -0.399 -0.489
27 C26 C C26 N Y N 0 5.508 -0.326 0.069
28 C3' C C3' R N N 0 -2.94 -2.616 -0.213
29 C4' C C4' R N N 0 -4.086 -1.597 -0.044
30 C5' C C5' N N N 0 -4.524 -1.727 1.43
31 HN02 H HN02 N N N 0 -7.928 0.349 -2.421
32 HN0A H HN0A N N N 0 -8.693 1.727 -1.84
33 H03 H H03 N N N 0 -7.695 3.18 -0.195
34 H05 H H05 N N N 0 -3.813 2.041 1.185
35 H07 H H07 N N N 0 -6.145 3.699 2.483
36 H07A H H07A N N N 0 -4.692 4.294 1.645
37 H07B H H07B N N N 0 -6.308 4.768 1.07
38 H08 H H08 N N N 0 -3.124 -0.146 -1.314
39 H08A H H08A N N N 0 -2.845 0.1 0.426
40 HN1' H HN1' N N N 0 -4.766 -3.786 1.499
41 H10 H H10 N N N 0 -0.542 -3.629 -0.74
42 H10A H H10A N N N 0 -1.307 -3.088 -2.254
43 H11 H H11 N N N 0 1.077 -2.535 -2.32
44 H11A H H11A N N N 0 0.133 -1.031 -2.19
45 HN12 H HN12 N N N 0 0.536 -1.114 0.205
46 H13 H H13 N N N 0 3.013 -1.403 -1.365
47 H13A H H13A N N N 0 2.07 0.101 -1.236
48 H2' H H2' N N N 0 -2.004 -2.773 1.748
49 H2'A H H2'A N N N 0 -2.552 -4.336 1.066
50 H22 H H22 N N N 0 3.298 2.199 0.412
51 H24 H H24 N N N 0 7.471 2.366 -0.473
52 H26 H H26 N N N 0 5.56 -1.403 0.111
53 H3' H H3' N N N 0 -3.203 -3.364 -0.961
54 H4' H H4' N N N 0 -4.912 -1.844 -0.71
55 H5' H H5' N N N 0 -5.606 -1.621 1.516
56 H5'A H H5'A N N N 0 -4.018 -0.982 2.045