Atom Nomenclature for BS2

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 BS2

Atom Name (V3) Atom Name (V2)
CAY CAY
CAL CAL
CAF CAF
CAD CAD
CAJ CAJ
CAW CAW
CAN CAN
CAO CAO
CAX CAX
CAK CAK
CAE CAE
CAG CAG
CAM CAM
CAZ CAZ
CBD CBD
OAU OAU
CBA CBA
CAT CAT
CAS CAS
CBB CBB
CAP CAP
CAQ CAQ
CBC CBC
NBE NBE
CAR CAR
CAV CAV
CAH CAH
CAB CAB
CAA CAA
CAC CAC
CAI CAI
HAL HAL
HBD HBD
HAF HAF
HAD HAD
HAJ HAJ
HAN1 HAN1
HAN2 HAN2
HAO1 HAO1
HAO2 HAO2
HAK HAK
HAE HAE
HAG HAG
HAM HAM
HBA HBA
HAT1 HAT1
HAT2 HAT2
HAS1 HAS1
HAS2 HAS2
HBC HBC
HBB HBB
HAP1 HAP1
HAP2 HAP2
HAQ1 HAQ1
HAQ2 HAQ2
HAR1 HAR1
HAR2 HAR2
HAH HAH
HAI HAI
HAB HAB
HAA HAA
HAC HAC
HBE HBE