Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UPE

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 53


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -6.729 1.974 -0.098
2 N1 N N1 N N N 0 -0.736 -1.078 0.044
3 C2 C C2 N N N 0 -0.856 -1.031 1.38
4 O2 O O2 N N N 0 -1.955 -1.184 1.877
5 N3 N N3 N N N 0 0.198 -0.82 2.186
6 C4 C C4 N N N 0 1.432 -0.647 1.666
7 O4 O O4 N N N 0 2.391 -0.456 2.391
8 C5 C C5 N N N 0 1.592 -0.694 0.204
9 C6 C C6 N N N 0 0.467 -0.914 -0.566
10 C1' C C1' R N N 0 -1.927 -1.317 -0.774
11 C2' C C2' N N N 0 -2.541 -2.695 -0.44
12 C21 C C21 N N N 0 2.911 -0.512 -0.419
13 O22 O O22 N N N 0 3.042 -0.656 -1.62
14 N23 N N23 N N N 0 3.976 -0.185 0.34
15 C24 C C24 N N N 0 5.265 0.106 -0.292
16 C25 C C25 N N N 0 6.297 0.445 0.786
17 C26 C C26 N Y N 0 7.623 0.744 0.136
18 C27 C C27 N Y N 0 7.932 2.038 -0.241
19 C28 C C28 N Y N 0 9.148 2.312 -0.837
20 C29 C C29 N Y N 0 10.056 1.293 -1.057
21 C3' C C3' S N N 0 -4.065 -2.458 -0.528
22 O3' O O3' N N N 0 -4.642 -3.282 -1.544
23 C30 C C30 N Y N 0 9.747 -0.0010 -0.681
24 C31 C C31 N Y N 0 8.532 -0.274 -0.079
25 C4' C C4' R N N 0 -4.192 -0.966 -0.905
26 O4' O O4' N N N 0 -2.962 -0.364 -0.447
27 C5' C C5' N N N 0 -5.39 -0.336 -0.191
28 O5' O O5' N N N 0 -5.56 1.009 -0.64
29 OP1 O OP1 N N N 0 -8.041 1.317 -0.291
30 OP2 O OP2 N N N 0 -6.5 2.266 1.469
31 OP3 O OP3 N N Y 0 -6.699 3.363 -0.912
32 HN3 H HN3 N N N 0 0.072 -0.792 3.147
33 H6 H H6 N N N 0 0.542 -0.956 -1.643
34 H1' H H1' N N N 0 -1.677 -1.258 -1.833
35 H2' H H2' N N N 0 -2.227 -3.44 -1.172
36 H2'A H H2'A N N N 0 -2.26 -3.005 0.566
37 HN23 H HN23 N N N 0 3.888 -0.143 1.306
38 H24 H H24 N N N 0 5.6 -0.767 -0.853
39 H24A H H24A N N N 0 5.155 0.953 -0.969
40 H25 H H25 N N N 0 5.962 1.318 1.347
41 H25A H H25A N N N 0 6.407 -0.402 1.463
42 H27 H H27 N N N 0 7.223 2.834 -0.069
43 H28 H H28 N N N 0 9.39 3.323 -1.131
44 H29 H H29 N N N 0 11.006 1.507 -1.524
45 H3' H H3' N N N 0 -4.538 -2.651 0.435
46 HO3' H HO3' N N N 0 -4.537 -4.23 -1.388
47 H30 H H30 N N N 0 10.455 -0.798 -0.854
48 H31 H H31 N N N 0 8.293 -1.284 0.219
49 H4' H H4' N N N 0 -4.291 -0.854 -1.984
50 H5' H H5' N N N 0 -6.289 -0.911 -0.415
51 H5'A H H5'A N N N 0 -5.215 -0.341 0.885
52 HOP2 H HOP2 N N N 0 -5.658 2.697 1.67
53 HOP3 H HOP3 N N Y 0 -7.378 3.995 -0.637