Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PDBeChem : Atoms of Molecule

 Molecule : D70

Atoms of a chemical element, that composes a molecule

Total Number of Atoms: 115


Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P PA N N N 0 5.506 3.08 -0.854
2 O1A O O1A N N N 0 6.216 3.162 -2.296
3 O2A O O2A N N N 0 5.532 4.415 -0.214
4 O5B O O5B N N N 0 6.294 2.026 0.073
5 C5B C C5B N N N 0 7.642 2.224 0.504
6 C4B C C4B R N N 0 8.082 1.038 1.365
7 O4B O O4B N N N 0 8.146 -0.152 0.562
8 C3B C C3B S N N 0 9.496 1.291 1.923
9 O3B O O3B N N N 0 9.476 1.294 3.352
10 C2B C C2B R N N 0 10.331 0.1 1.395
11 O2B O O2B N N N 0 11.223 -0.384 2.401
12 C1B C C1B R N N 0 9.236 -0.949 1.075
13 N9A N N9A N Y N 0 9.707 -1.894 0.06
14 C8A C C8A N Y N 0 9.563 -1.766 -1.289
15 N7A N N7A N Y N 0 10.099 -2.788 -1.892
16 C5A C C5A N Y N 0 10.619 -3.633 -0.97
17 C6A C C6A N Y N 0 11.299 -4.861 -1.029
18 N6A N N6A N N N 0 11.57 -5.464 -2.245
19 N1A N N1A N Y N 0 11.677 -5.431 0.111
20 C2A C C2A N Y N 0 11.424 -4.863 1.276
21 N3A N N3A N Y N 0 10.79 -3.714 1.379
22 C4A C C4A N Y N 0 10.378 -3.068 0.293
23 N1 N N1 N N N 0 -5.578 -0.64 -1.994
24 C2 C C2 N N N 0 -5.775 -1.839 -2.576
25 O2 O O2 N N N 0 -5.78 -1.916 -3.789
26 N3 N N3 N N N 0 -5.968 -2.954 -1.849
27 C4 C C4 N N N 0 -6.254 -2.888 -0.531
28 O4 O O4 N N N 0 -6.352 -3.899 0.131
29 C4X C C4X S N N 0 -6.447 -1.537 0.1
30 N5 N N5 N N N 0 -6.136 -1.563 1.536
31 C5X C C5X N Y N 0 -5.902 -0.313 2.144
32 C6 C C6 N Y N 0 -5.864 -0.23 3.527
33 C7 C C7 N Y N 0 -5.638 0.989 4.141
34 C7M C C7M N N N 0 -5.596 1.08 5.644
35 C8 C C8 N Y N 0 -5.448 2.124 3.374
36 C8M C C8M N N N 0 -5.202 3.45 4.045
37 C9 C C9 N Y N 0 -5.483 2.047 1.995
38 C9A C C9A N Y N 0 -5.71 0.827 1.367
39 N10 N N10 N N N 0 -5.737 0.789 -0.034
40 C10 C C10 S N N 0 -5.459 -0.553 -0.543
41 C1' C C1' N N N 0 -4.807 1.772 -0.606
42 C2' C C2' S N N 0 -3.369 1.362 -0.281
43 O2' O O2' N N N 0 -3.185 1.353 1.136
44 C3' C C3' S N N 0 -2.399 2.362 -0.914
45 O3' O O3' N N N 0 -2.582 2.372 -2.331
46 C4' C C4' R N N 0 -0.961 1.953 -0.588
47 O4' O O4' N N N 0 -0.777 1.943 0.829
48 C5' C C5' N N N 0 0.009 2.953 -1.221
49 O5' O O5' N N N 0 1.352 2.508 -1.017
50 P P P N N N 0 2.635 3.319 -1.552
51 O1P O O1P N N N 0 2.589 4.708 -1.042
52 O2P O O2P N N N 0 2.625 3.338 -3.162
53 O3P O O3P N N N 0 3.979 2.601 -1.033
54 CAH C CAH N Y N 0 -9.536 -1.69 1.662
55 CAD C CAD N Y N 0 -10.409 -2.59 2.245
56 CAB C CAB N Y N 0 -10.583 -3.844 1.689
57 CAE C CAE N Y N 0 -9.884 -4.198 0.55
58 CAI C CAI N Y N 0 -9.011 -3.298 -0.033
59 CAP C CAP N Y N 0 -8.837 -2.045 0.523
60 CAM C CAM S N N 0 -7.886 -1.064 -0.113
61 CAL C CAL N N N 0 -8.176 -0.971 -1.612
62 CAO C CAO N N N 0 -9.556 -0.403 -1.823
63 NAA N NAA N N N 0 -10.278 -0.085 -0.816
64 CAN C CAN N N N 0 -10.086 -0.209 -3.221
65 CAQ C CAQ N N N 0 -11.497 0.377 -3.155
66 H1A H H1A N N N 0 6.234 2.321 -2.774
67 H5B1 H H5B1 N N N 0 8.294 2.302 -0.366
68 H5B2 H H5B2 N N N 0 7.706 3.141 1.089
69 H4B H H4B N N N 0 7.378 0.894 2.185
70 H3B H H3B N N N 0 9.891 2.234 1.546
71 H1B H H1B N N N 0 8.933 -1.475 1.981
72 HA H HA N N N 0 10.341 1.449 3.757
73 H2B H H2B N N N 0 10.878 0.378 0.494
74 HB H HB N N N 0 11.871 0.269 2.699
75 H8A H H8A N N N 0 9.076 -0.94 -1.785
76 H6A1 H H6A1 N N N 0 11.289 -5.039 -3.07
77 H6A2 H H6A2 N N N 0 12.04 -6.312 -2.272
78 H2A H H2A N N N 0 11.749 -5.36 2.178
79 H1 H H1 N N N 0 -5.512 0.161 -2.537
80 H10 H H10 N N N 0 -4.445 -0.829 -0.254
81 H3 H H3 N N N 0 -5.899 -3.821 -2.279
82 H5 H H5 N N N 0 -6.095 -2.393 2.037
83 HAM H HAM N N N 0 -8.017 -0.083 0.343
84 H6 H H6 N N N 0 -6.013 -1.116 4.126
85 H7M1 H H7M1 N N N 0 -4.575 0.922 5.99
86 H7M2 H H7M2 N N N 0 -5.938 2.066 5.958
87 H7M3 H H7M3 N N N 0 -6.247 0.317 6.072
88 H8M1 H H8M1 N N N 0 -4.131 3.59 4.191
89 H8M2 H H8M2 N N N 0 -5.591 4.252 3.418
90 H8M3 H H8M3 N N N 0 -5.705 3.467 5.012
91 H9 H H9 N N N 0 -5.334 2.938 1.403
92 H1'1 H H1'1 N N N 0 -4.938 1.81 -1.687
93 H1'2 H H1'2 N N N 0 -5.01 2.754 -0.18
94 H2' H H2' N N N 0 -3.176 0.366 -0.679
95 HC H HC N N N 0 -3.24 2.227 1.546
96 H3' H H3' N N N 0 -2.592 3.358 -0.515
97 HD H HD N N N 0 -2.427 1.516 -2.753
98 H4' H H4' N N N 0 -0.767 0.957 -0.987
99 HE H HE N N N 0 -0.933 2.799 1.252
100 H5'1 H H5'1 N N N 0 -0.191 3.026 -2.29
101 H5'2 H H5'2 N N N 0 -0.124 3.931 -0.759
102 H2P H H2P N N N 0 2.654 2.46 -3.566
103 HAH H HAH N N N 0 -9.404 -0.709 2.093
104 HAD H HAD N N N 0 -10.955 -2.313 3.135
105 HAB H HAB N N N 0 -11.264 -4.547 2.145
106 HAE H HAE N N N 0 -10.019 -5.178 0.116
107 HAI H HAI N N N 0 -8.465 -3.575 -0.922
108 HAL1 H HAL1 N N N 0 -7.44 -0.322 -2.086
109 HAL2 H HAL2 N N N 0 -8.121 -1.966 -2.055
110 HAA H HAA N N N 0 -11.166 0.28 -0.952
111 HAN1 H HAN1 N N N 0 -9.434 0.474 -3.765
112 HAQ3 H HAQ3 N N N 0 -11.468 1.338 -2.641
113 HAN2 H HAN2 N N N 0 -10.115 -1.17 -3.735
114 HAQ1 H HAQ1 N N N 0 -11.88 0.517 -4.166
115 HAQ2 H HAQ2 N N N 0 -12.149 -0.306 -2.611