Chemical Components in the PDB

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PDBeChem : Atoms of Molecule

 Molecule : APR

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 59


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 2.348 -0.932 9.041
2 C2 C C2 N Y N 0 1.265 -1.622 8.731
3 N3 N N3 N Y N 0 0.592 -1.418 7.618
4 C4 C C4 N Y N 0 0.984 -0.493 6.749
5 C5 C C5 N Y N 0 2.128 0.271 7.035
6 C6 C C6 N Y N 0 2.816 0.012 8.233
7 N6 N N6 N N N 0 3.952 0.73 8.566
8 N7 N N7 N Y N 0 2.307 1.124 5.999
9 C8 C C8 N Y N 0 1.365 0.943 5.12
10 N9 N N9 N Y N 0 0.523 -0.044 5.537
11 C1' C C1* R N N 0 -0.656 -0.537 4.822
12 C2' C C2* R N N 0 -1.902 0.29 5.207
13 O2' O O2* N N N 0 -2.672 -0.385 6.202
14 C3' C C3* S N N 0 -2.7 0.4 3.886
15 O3' O O3* N N N 0 -3.986 -0.206 4.025
16 O4' O O4* N N N 0 -0.502 -0.338 3.4
17 C4' C C4* R N N 0 -1.842 -0.377 2.863
18 C5' C C5* N N N 0 -1.888 0.307 1.496
19 O5' O O5* N N N 0 -1.032 -0.386 0.586
20 PA P PA S N N 0 -1.129 0.384 -0.823
21 O1A O O1A N N N 0 -0.686 1.786 -0.651
22 O2A O O2A N N N 0 -2.652 0.362 -1.343
23 O3A O O3A N N N 0 -0.183 -0.348 -1.901
24 PB P PB R N N 0 -0.328 0.47 -3.28
25 O1B O O1B N N N 0 0.101 1.871 -3.069
26 O2B O O2B N N N 0 -1.865 0.447 -3.758
27 O5D O RO5* N N N 0 0.595 -0.21 -4.408
28 C5D C RC5* N N N 0 0.423 0.556 -5.601
29 O4D O RO4* N N N 0 0.853 -1.385 -6.996
30 O1D O RO1* N N N 0 0.208 -2.68 -8.863
31 C1D C RC1* R N N 0 1.03 -1.602 -8.412
32 C3D C RC3* S N N 0 1.096 0.775 -8.014
33 O2D O RO2* N N N 0 1.185 -0.064 -10.319
34 C2D C RC2* R N N 0 0.574 -0.261 -9.042
35 O3D O RO3* N N N 0 2.341 1.326 -8.446
36 C4D C RC4* R N N 0 1.279 -0.041 -6.72
37 H2 H H2 N N N 0 0.918 -2.381 9.417
38 H61 H 1H6 N N N 0 4.416 0.544 9.397
39 H62 H 2H6 N N N 0 4.286 1.415 7.966
40 H8 H H8 N N N 0 1.265 1.493 4.196
41 H'1 H 1H* N N N 0 -0.819 -1.592 5.042
42 H'2 H 2H* N N N 0 -1.608 1.279 5.559
43 HO'2 H 2HO* N N N 0 -3.464 0.149 6.354
44 H'3 H 3H* N N N 0 -2.801 1.443 3.585
45 HO'3 H 3HO* N N N 0 -4.474 0.319 4.673
46 H'4 H 4H* N N N 0 -2.189 -1.407 2.782
47 H5'1 H 1H5* N N N 0 -2.91 0.293 1.116
48 H5'2 H 2H5* N N N 0 -1.552 1.34 1.595
49 HOA2 H 2HOA N N N 0 -2.901 -0.566 -1.442
50 HOB2 H 2HOB N N N 0 -2.105 -0.48 -3.884
51 H5R1 H 1H5R N N N 0 -0.625 0.539 -5.897
52 H5R2 H 2H5R N N N 0 0.732 1.586 -5.418
53 HOR1 H 1HOR N N N 0 0.495 -3.469 -8.385
54 HR'1 H 1HR* N N N 0 2.078 -1.797 -8.642
55 HOR2 H 2HOR N N N 0 0.892 -0.792 -10.884
56 HR'2 H 2HR* N N N 0 -0.512 -0.219 -9.122
57 HOR3 H 3HOR N N N 0 2.172 1.772 -9.288
58 HR'3 H 3HR* N N N 0 0.361 1.567 -7.864
59 HR'4 H 4HR* N N N 0 2.329 -0.038 -6.425