Atom Nomenclature for B12

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for B12

Atom Name (V3) Atom Name (V2)
CO CO
N21 N21
N22 N22
N23 N23
N24 N24
C1 C1
C20 C20
C2 C2
C25 C25
C26 C26
C27 C27
O28 O28
N29 N29
C3 C3
C30 C30
C31 C31
C32 C32
O34 O34
N33 N33
C4 C4
C5 C5
C35 C35
C6 C6
C7 C7
C36 C36
C37 C37
C38 C38
O39 O39
N40 N40
C8 C8
C41 C41
C42 C42
C43 C43
O44 O44
N45 N45
C9 C9
C10 C10
C11 C11
C12 C12
C46 C46
C47 C47
C13 C13
C48 C48
C49 C49
C50 C50
O51 O51
N52 N52
C14 C14
C15 C15
C53 C53
C16 C16
C17 C17
C54 C54
C55 C55
C56 C56
C57 C57
O58 O58
N59 N59
C18 C18
C60 C60
C61 C61
O63 O63
N62 N62
C19 C19
C1P C1P
C2P C2P
C3P C3P
O3 O3
O4 O4
O5 O5
P P
O2 O2
C3R C3R
C2R C2R
O7R O7R
C1R C1R
O6R O6R
C4R C4R
C5R C5R
O8R O8R
N1B N1B
C8B C8B
C2B C2B
N3B N3B
C9B C9B
C4B C4B
C5B C5B
C5M C5M
C6B C6B
C6M C6M
C7B C7B
H201 H201
H202 H202
H203 H203
H251 H251
H252 H252
H253 H253
H261 H261
H262 H262
H291 H291
H292 H292
H3 H3
H301 H301
H302 H302
H311 H311
H312 H312
H331 H331
H332 H332
H351 H351
H352 H352
H353 H353
H361 H361
H362 H362
H363 H363
H371 H371
H372 H372
H401 H401
H402 H402
H8 H8
H411 H411
H412 H412
H421 H421
H422 H422
H451 H451
H452 H452
H10 H10
H461 H461
H462 H462
H463 H463
H471 H471
H472 H472
H473 H473
H13 H13
H481 H481
H482 H482
H491 H491
H492 H492
H521 H521
H522 H522
H531 H531
H532 H532
H533 H533
H541 H541
H542 H542
H543 H543
H551 H551
H552 H552
H561 H561
H562 H562
H59 H59
H18 H18
H601 H601
H602 H602
H621 H621
H622 H622
H1P1 H1P1
H1P2 H1P2
H2P H2P
H3P1 H3P1
H3P2 H3P2
H3P3 H3P3
HOP5 HOP5
H3R H3R
H2R H2R
HOR7 HOR7
H1R H1R
H4R H4R
H5R1 H5R1
H5R2 H5R2
HOR8 HOR8
H2B H2B
H4B H4B
HM51 HM51
HM52 HM52
HM53 HM53
HM61 HM61
HM62 HM62
HM63 HM63
H7B H7B
H91 H91