Atom Nomenclature for 9PE

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 9PE

Atom Name (V3) Atom Name (V2)
P P
N N
O11 O11
O12 O12
O13 O13
O14 O14
C11 C11
C12 C12
C1 C1
C2 C2
C3 C3
O31 O31
O32 O32
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
O21 O21
O22 O22
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C2A C2A
C2B C2B
C2C C2C
C2D C2D
C2E C2E
C2F C2F
C2G C2G
C2H C2H
C2I C2I
HN HN
HNA HNA
HO14 HO14
H11 H11
H11A H11A
H12 H12
H12A H12A
H1 H1
H1A H1A
H2 H2
H3 H3
H3A H3A
H32 H32
H32A H32A
H33 H33
H33A H33A
H34 H34
H34A H34A
H35 H35
H35A H35A
H36 H36
H36A H36A
H37 H37
H37A H37A
H37B H37B
H22 H22
H22A H22A
H23 H23
H23A H23A
H24 H24
H24A H24A
H25 H25
H25A H25A
H26 H26
H26A H26A
H27 H27
H27A H27A
H28 H28
H28A H28A
H29 H29
H29A H29A
H2A H2A
H2AA H2AA
H2B H2B
H2BA H2BA
H2C H2C
H2CA H2CA
H2D H2D
H2DA H2DA
H2E H2E
H2EA H2EA
H2F H2F
H2FA H2FA
H2G H2G
H2GA H2GA
H2H H2H
H2HA H2HA
H2I H2I
H2IA H2IA
H2IB H2IB