Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : 18Y

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 87


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C3 C C3 N N N 0 -6.798 -2.08 -1.365
2 C5 C C5 N Y N 0 -3.113 1.331 2.166
3 O1 O O1 N N N 0 -3.645 -2.69 -2.745
4 C7' C C7' N N N 0 4.998 -3.039 0.788
5 O7' O O7' N N N 0 5.142 -1.841 0.847
6 C8' C C8' N N N 0 6.203 -3.939 0.687
7 C1 C C1 N N N 0 -4.416 -2.448 -1.84
8 C2 C C2 N N N 0 -5.758 -3.141 -1.748
9 C4 C C4 N N N 0 -6.482 -1.542 0.028
10 C6 C C6 N Y N 0 -1.841 1.808 2.252
11 C7 C C7 N Y N 0 -0.84 1.38 1.378
12 O8 O O8 N N N 0 -0.177 0.014 -0.449
13 C8 C C8 N Y N 0 -1.127 0.453 0.402
14 O9 O O9 N N N 0 -1.821 -1.43 -1.573
15 C9 C C9 N Y N 0 -2.767 -0.993 -0.707
16 O10 O O10 N N N 0 -5.719 0.31 1.931
17 C19 C C19 N Y N 0 -4.757 -0.116 1.069
18 O11 O O11 N N N 0 0.64 3.175 0.766
19 C11 C C11 S N N 0 0.539 1.953 1.527
20 O12 O O12 N N N 0 2.598 2.045 0.516
21 C12 C C12 S N N 0 1.605 1.022 0.9
22 O13 O O13 N N N 0 2.025 -0.285 -1.12
23 C13 C C13 S N N 0 1.095 0.609 -0.506
24 O14 O O14 N N N 0 1.857 1.906 -2.441
25 C14 C C14 S N N 0 1.06 1.962 -1.257
26 C15 C C15 R N N 0 1.686 2.936 -0.212
27 C25 C C25 N N N 0 2.331 4.197 -0.79
28 O1' O O1' N N N 0 2.585 -1.446 0.825
29 C1' C C1' S N N 0 2.083 -1.574 -0.507
30 C2' C C2' N N N 0 3.013 -2.483 -1.316
31 O3' O O3' N N N 0 4.042 -4.673 -1.328
32 C3' C C3' R N N 0 3.118 -3.843 -0.62
33 O4' O O4' N N N 0 3.646 -4.889 1.497
34 C4' C C4' S N N 0 3.614 -3.633 0.815
35 C5' C C5' S N N 0 2.66 -2.681 1.541
36 C6' C C6' N N N 0 1.269 -3.312 1.618
37 C20 C C20 N Y N 0 -4.077 -1.472 -0.795
38 C21 C C21 N Y N 0 -5.068 -1.027 0.104
39 C18 C C18 N N N 0 -1.505 2.822 3.315
40 C22 C C22 N Y N 0 -2.44 -0.052 0.287
41 C23 C C23 N Y N 0 -3.444 0.391 1.18
42 C24 C C24 N N N 0 -6.475 1.459 1.543
43 O26 O O26 N N N 0 1.341 4.967 -1.475
44 C27 C C27 N N N 0 1.88 5.96 -2.35
45 C28 C C28 N N N 0 3.848 5.944 -0.163
46 C17 C C17 N N N 0 -0.378 2.366 -1.584
47 O16 O O16 N N N 0 2.891 4.975 0.27
48 H3A H H3A N N N 0 -6.768 -1.264 -2.086
49 H3B H H3B N N N 0 -7.792 -2.529 -1.364
50 H5 H H5 N N N 0 -3.868 1.678 2.858
51 H81' H H81' N N N 0 7.109 -3.333 0.681
52 H82' H H82' N N N 0 6.223 -4.615 1.541
53 H83' H H83' N N N 0 6.147 -4.518 -0.235
54 H2B H H2B N N N 0 -5.723 -3.918 -0.984
55 H2A H H2A N N N 0 -6.015 -3.58 -2.712
56 H4A H H4A N N N 0 -7.171 -0.73 0.262
57 H4B H H4B N N N 0 -6.611 -2.34 0.758
58 H9 H H9 N N N 0 -1.342 -2.213 -1.27
59 H11 H H11 N N N 0 0.762 2.13 2.579
60 H12 H H12 N N N 0 1.954 0.207 1.534
61 H1 H H1 N N N 0 1.868 2.73 -2.947
62 H16 H H16 N N N 0 3.119 3.915 -1.489
63 H1' H H1' N N N 0 1.084 -2.01 -0.479
64 H2' H H2' N N N 0 2.609 -2.617 -2.319
65 H2 H H2 N N N 0 4.002 -2.028 -1.378
66 HO3 H HO3 N N N 0 3.793 -4.841 -2.247
67 H3' H H3' N N N 0 2.138 -4.32 -0.602
68 H4' H H4' N N N 0 3.949 -4.83 2.413
69 H5' H H5' N N N 0 3.031 -2.494 2.549
70 H61' H H61' N N N 0 0.898 -3.499 0.61
71 H62' H H62' N N N 0 1.327 -4.253 2.165
72 H63' H H63' N N N 0 0.59 -2.633 2.135
73 H61A H H61A N N N 0 -1.184 2.306 4.22
74 H63A H H63A N N N 0 -0.703 3.468 2.96
75 H62A H H62A N N N 0 -2.387 3.424 3.534
76 H111 H H111 N N N 0 -7.207 1.69 2.318
77 H112 H H112 N N N 0 -5.805 2.307 1.411
78 H113 H H113 N N N 0 -6.992 1.254 0.605
79 H62B H H62B N N N 0 1.119 6.261 -3.07
80 H63B H H63B N N N 0 2.191 6.827 -1.768
81 H61B H H61B N N N 0 2.74 5.55 -2.879
82 H63C H H63C N N N 0 4.354 6.368 0.705
83 H61C H H61C N N N 0 4.58 5.466 -0.813
84 H62C H H62C N N N 0 3.339 6.738 -0.71
85 H171 H H171 N N N 0 -0.948 2.463 -0.66
86 H172 H H172 N N N 0 -0.376 3.32 -2.112
87 H3 H H3 N N N 0 -0.836 1.603 -2.215