Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Atoms of Molecule

 Molecule : C5X

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 34


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -0.15 0.151 0.944
2 C2 C C2 R N N 0 -1.057 -0.244 2.111
3 C3 C C3 S N N 0 -0.447 0.274 3.419
4 C4 C C4 R N N 0 0.999 -0.223 3.516
5 C5 C C5 N N N 0 1.75 0.17 2.242
6 O1 O O1 N N N 0 -0.728 -0.303 -0.28
7 O2 O O2 N N N 0 -2.353 0.328 1.926
8 O3 O O3 N N N 0 -1.204 -0.214 4.528
9 O4 O O4 N N N 0 1.634 0.371 4.649
10 O5 O O5 N N N 0 1.136 -0.441 1.11
11 C1' C C1' N N N 0 0.154 0.099 -1.329
12 C2' C C2' N N N 0 -0.409 -0.359 -2.675
13 C3' C C3' N N N 0 0.536 0.071 -3.798
14 C4' C C4' R N N 0 -0.027 -0.387 -5.144
15 C5' C C5' N N N 0 0.757 -0.025 -6.406
16 O' O O' N N N 0 -0.471 0.618 -6.057
17 H1 H H1 N N N 0 -0.048 1.236 0.916
18 H2 H H2 N N N 0 -1.141 -1.33 2.156
19 H3 H H3 N N N 0 -0.457 1.364 3.42
20 H4 H H4 N N N 0 1.005 -1.308 3.622
21 H51 H H51 N N N 0 1.725 1.254 2.127
22 H52 H H52 N N N 0 2.786 -0.16 2.315
23 HO2 H HO2 N N Y 0 -2.696 -0.02 1.091
24 HO3 H HO3 N N Y 0 -0.786 0.135 5.327
25 HO4 H HO4 N N Y 0 2.54 0.034 4.671
26 H1'1 H H1'1 N N N 0 0.25 1.184 -1.326
27 H1'2 H H1'2 N N N 0 1.134 -0.352 -1.172
28 H2'1 H H2'1 N N N 0 -0.505 -1.445 -2.678
29 H2'2 H H2'2 N N N 0 -1.388 0.091 -2.831
30 H3'1 H H3'1 N N N 0 0.632 1.157 -3.795
31 H3'2 H H3'2 N N N 0 1.516 -0.38 -3.641
32 H4' H H4' N N N 0 -0.562 -1.336 -5.134
33 H5'1 H H5'1 N N N 0 1.68 0.542 -6.285
34 H5'2 H H5'2 N N N 0 0.742 -0.733 -7.234