Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : H2U

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 36


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 -1.087 0.031 -3.989
2 OP1 O O1P N N N 0 -1.678 -1.272 -3.613
3 OP2 O O2P N N N 0 -2.235 0.986 -4.593
4 OP3 O O3P N N Y 0 0.058 -0.197 -5.097
5 O5' O O5* N N N 0 -0.444 0.725 -2.687
6 C5' C C5* N N N 0 0.561 -0.164 -2.199
7 C4' C C4* R N N 0 1.216 0.437 -0.955
8 O4' O O4* N N N 0 0.236 0.615 0.093
9 C3' C C3* S N N 0 2.255 -0.538 -0.359
10 O3' O O3* N N N 0 3.574 -0.183 -0.778
11 C1' C C1* R N N 0 0.997 0.702 1.318
12 C2' C C2* R N N 0 2.107 -0.361 1.168
13 O2' O O2* N N N 0 3.331 0.104 1.739
14 N1 N N1 N N N 0 0.148 0.394 2.471
15 C2 C C2 N N N 0 -0.524 -0.766 2.507
16 O2 O O2 N N N 0 -0.332 -1.59 1.633
17 N3 N N3 N N N 0 -1.397 -1.045 3.489
18 C4 C C4 N N N 0 -1.818 -0.085 4.333
19 O4 O O4 N N N 0 -2.546 -0.368 5.26
20 C5 C C5 N N N 0 -1.384 1.343 4.125
21 C6 C C6 N N N 0 0.04 1.36 3.566
22 HOP2 H 2HOP N N N 0 -2.593 0.534 -5.37
23 HOP3 H 3HOP N N N 0 0.415 0.674 -5.313
24 H5' H 1H5* N N N 0 1.317 -0.316 -2.97
25 H5'' H 2H5* N N N 0 0.106 -1.121 -1.943
26 H4' H H4* N N N 0 1.688 1.389 -1.198
27 H3' H H3* N N N 0 2.026 -1.563 -0.649
28 HO3' H *HO3 N N Y 0 4.18 -0.805 -0.353
29 H1' H H1* N N N 0 1.435 1.694 1.423
30 H2' H H2* N N N 0 1.803 -1.299 1.633
31 HO2' H *HO2 N N N 0 3.998 -0.572 1.562
32 HN3 H HN3 N N N 0 -1.731 -1.95 3.591
33 H51 H 1H5 N N N 0 -1.408 1.874 5.076
34 H52 H 2H5 N N N 0 -2.057 1.829 3.419
35 H61 H 1H6 N N N 0 0.743 1.094 4.356
36 H62 H 2H6 N N N 0 0.273 2.358 3.194