Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Atoms of Molecule

 Molecule : PYO

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 33


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 -1.825 1.007 -4.603
2 P P P N N N 0 -0.773 0.044 -3.855
3 OP1 O O1P N N N 0 0.502 -0.196 -4.805
4 OP2 O O2P N N N 0 -1.419 -1.253 -3.557
5 O5' O O5* N N N 0 -0.297 0.735 -2.481
6 C5' C C5* N N N 0 0.629 -0.163 -1.867
7 C4' C C4* R N N 0 1.123 0.436 -0.549
8 O4' O O4* N N N 0 0.018 0.625 0.364
9 C3' C C3* S N N 0 2.068 -0.547 0.176
10 C1' C C1* R N N 0 0.615 0.707 1.676
11 O3' O O3* N N N 0 3.433 -0.205 -0.07
12 C2' C C2* R N N 0 1.726 -0.366 1.672
13 O2' O O2* N N N 0 2.87 0.089 2.395
14 N1 N N1 N N N 0 -0.377 0.409 2.711
15 C6 C C6 N N N 0 -0.606 1.302 3.708
16 C2 C C2 N N N 0 -1.066 -0.746 2.668
17 C5 C C5 N N N 0 -1.531 1.01 4.661
18 O2 O O2 N N N 0 -0.852 -1.54 1.767
19 N3 N N3 N N N 0 -1.972 -1.041 3.603
20 C4 C C4 N N N 0 -2.223 -0.201 4.588
21 HOP3 H 3HOP N N N 0 -2.084 0.558 -5.419
22 HOP1 H 1HOP N N N 0 0.893 0.671 -4.975
23 H5'' H 2H5* N N N 0 0.136 -1.115 -1.671
24 H5' H 1H5* N N N 0 1.476 -0.322 -2.534
25 H4' H H4* N N N 0 1.631 1.383 -0.731
26 H3' H H3* N N N 0 1.869 -1.571 -0.14
27 H1' H H1* N N N 0 1.044 1.696 1.836
28 HO3 H 3HO N N Y 0 3.973 -0.831 0.43
29 H2' H H2* N N N 0 1.356 -1.3 2.094
30 HO2 H 2HO N N N 0 3.548 -0.593 2.306
31 HC4 H HC4 N N N 0 -2.962 -0.45 5.336
32 HC6 H HC6 N N N 0 -0.059 2.233 3.745
33 HC5 H HC5 N N N 0 -1.729 1.706 5.464