Atom Nomenclature for PYH

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 PYH

Atom Name (V3) Atom Name (V2)
CAA CAA
CAP CAP
CAJ CAJ
CAF CAF
NAL NAL
CAR CAR
CAO CAO
OAD OAD
NZ NZ
CE CE
CD CD
CG CG
CB CB
CA CA
C C
OXT OXT
O O
N N
HXT HXT
HA HA
H H
HN2 HN2
HB1 HB1
HB2 HB2
HG1 HG1
HG2 HG2
HD1 HD1
HD2 HD2
HE1 HE1
HE2 HE2
HZ HZ
HAR HAR
HAF HAF
HAJ1 HAJ1
HAJ2 HAJ2
HAP HAP
HAA1 HAA1
HAA2 HAA2
HAA3 HAA3