Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : UPG

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 60


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 4.871 -1.188 0.165
2 C2 C C2 N N N 0 5.434 -2.195 0.857
3 N3 N N3 N N N 0 5.677 -3.384 0.274
4 C4 C C4 N N N 0 5.358 -3.583 -1.021
5 C5 C C5 N N N 0 4.766 -2.532 -1.76
6 C6 C C6 N N N 0 4.533 -1.35 -1.151
7 O2 O O2 N N N 0 5.726 -2.03 2.026
8 O4 O O4 N N N 0 5.579 -4.658 -1.549
9 C1C C C1'A R N N 0 4.613 0.093 0.828
10 C2C C C2'A R N N 0 5.477 1.216 0.201
11 O2C O O2'A N N N 0 6.766 1.271 0.814
12 C3C C C3'A S N N 0 4.653 2.484 0.534
13 C4C C C4'A R N N 0 3.231 1.951 0.799
14 O4C O O4'A N N N 0 3.26 0.53 0.58
15 O3C O O3'A N N N 0 5.171 3.126 1.7
16 C5C C C5'A N N N 0 2.242 2.606 -0.167
17 O5C O O5'A N N N 0 0.913 2.195 0.161
18 PA P PA N N N 0 -0.385 2.693 -0.651
19 O1A O O1A N N N 0 -0.213 2.389 -2.09
20 O2A O O2A N N N 0 -0.563 4.281 -0.456
21 O3A O O3A N N N 0 -1.691 1.934 -0.095
22 PB P PB N N N 0 -3.161 1.656 -0.689
23 O1B O O1B N N N 0 -3.049 1.21 -2.095
24 O2B O O2B N N N 0 -4.031 3.009 -0.623
25 O3B O O3B N N N 0 -3.884 0.511 0.182
26 C1' C C1' R N N 0 -5.161 -0.034 -0.156
27 C2' C C2' R N N 0 -5.883 -0.473 1.12
28 C3' C C3' S N N 0 -5.071 -1.579 1.803
29 C4' C C4' S N N 0 -4.877 -2.736 0.818
30 C5' C C5' R N N 0 -4.194 -2.21 -0.447
31 C6' C C6' N N N 0 -4.051 -3.348 -1.46
32 O2' O O2' N N N 0 -6.009 0.642 2.005
33 O3' O O3' N N N 0 -5.774 -2.045 2.956
34 O4' O O4' N N N 0 -4.06 -3.742 1.419
35 O5' O O5' N N N 0 -4.985 -1.164 -1.014
36 O6' O O6' N N N 0 -3.31 -2.887 -2.592
37 HN3 H HN3 N N N 0 6.084 -4.099 0.787
38 H5 H H5 N N N 0 4.504 -2.673 -2.799
39 H6 H H6 N N N 0 4.081 -0.536 -1.699
40 H1C H H1'A N N N 0 4.804 0.015 1.899
41 H2C H H2'A N N N 0 5.567 1.082 -0.877
42 HO2C H HO2' N N N 0 7.344 1.959 0.456
43 H3C H H3'A N N N 0 4.651 3.171 -0.312
44 H4C H H4'A N N N 0 2.942 2.162 1.828
45 HO3C H HO3' N N N 0 6.085 3.429 1.609
46 H5C1 H H5'1 N N N 0 2.317 3.69 -0.085
47 H5C2 H H5'2 N N N 0 2.474 2.302 -1.188
48 HOA2 H HOA2 N N N 0 -0.681 4.554 0.465
49 HOB2 H HOB2 N N N 0 -4.146 3.36 0.271
50 H1' H H1' N N N 0 -5.755 0.722 -0.668
51 H2' H H2' N N N 0 -6.873 -0.851 0.867
52 H3' H H3' N N N 0 -4.099 -1.186 2.101
53 H4' H H4' N N N 0 -5.847 -3.16 0.558
54 H5' H H5' N N N 0 -3.207 -1.823 -0.193
55 H6'1 H H6'1 N N N 0 -3.524 -4.182 -0.997
56 H6'2 H H6'2 N N N 0 -5.04 -3.675 -1.781
57 HO2' H HO2A N N N 0 -6.508 1.383 1.636
58 HO3' H HO3A N N N 0 -5.938 -1.362 3.62
59 HO4' H HO4' N N N 0 -4.43 -4.117 2.23
60 HO6' H HO6' N N N 0 -3.181 -3.557 -3.277