Atom Nomenclature for FA9

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 FA9

Atom Name (V3) Atom Name (V2)
O4 O4
O2 O2
C4 C4
N3 N3
C2 C2
N1 N1
C10 C10
C4A C4A
C3B C3B
CB1 CB1
CB2 CB2
CB3 CB3
CB4 CB4
CB5 CB5
CB6 CB6
C2B C2B
C1B C1B
O1B O1B
N5 N5
C5A C5A
C6 C6
C7 C7
C7M C7M
C8 C8
C8M C8M
C9 C9
C9A C9A
N10 N10
C1' C1'
C2' C2'
O2' O2'
C3' C3'
O3' O3'
C4' C4'
O4' O4'
C5' C5'
O5' O5'
P P
O1P O1P
O2P O2P
O3P O3P
PA PA
O1A O1A
O2A O2A
OA5 OA5
CA5 CA5
CA4 CA4
OA4 OA4
CA3 CA3
OA3 OA3
CA2 CA2
OA2 OA2
CA1 CA1
N9A N9A
C8A C8A
N7A N7A
C5C C5C
C4C C4C
N3A N3A
C2A C2A
N1A N1A
C6A C6A
N6A N6A
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39
H40 H40
H41 H41
H42 H42
H43 H43
H30 H30