Atom Nomenclature for LY4

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 LY4

Atom Name (V3) Atom Name (V2)
CBD CBD
CBB CBB
NAW NAW
CAV CAV
CAX CAX
CAY CAY
CAZ CAZ
CAP CAP
CAO CAO
CAN CAN
CAM CAM
CAH CAH
CAE CAE
OAF OAF
NAD NAD
CAC CAC
OAB OAB
CAG CAG
CAL CAL
CAU CAU
CAK CAK
CAJ CAJ
CAI CAI
CAQ CAQ
CAR CAR
CAS CAS
NAT NAT
CBA CBA
CBC CBC
OBE OBE
CBF CBF
CBG CBG
NBH NBH
CBI CBI
CBJ CBJ
HBD1 1HBD
HBD2 2HBD
HBB1 1HBB
HBB2 2HBB
HAV HAV
HAY HAY
HAZ HAZ
HAP HAP
HAO HAO
HAD HAD
HAU HAU
HAJ HAJ
HAI HAI
HAQ HAQ
HAR HAR
HBA1 1HBA
HBA2 2HBA
HBC1 1HBC
HBC2 2HBC
HBF HBF
HBG1 1HBG
HBG2 2HBG
HBI1 1HBI
HBI2 2HBI
HBI3 3HBI
HBJ1 1HBJ
HBJ2 2HBJ
HBJ3 3HBJ