Atom Nomenclature for RX4

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 RX4

Atom Name (V3) Atom Name (V2)
CAX CAX
CAA CAA
OAE OAE
CBB CBB
OAI OAI
CBF CBF
CAR CAR
CAZ CAZ
OAK OAK
OAG OAG
NAU NAU
CAP CAP
CAN CAN
CAM CAM
CAO CAO
CAQ CAQ
CBC CBC
CAS CAS
CBG CBG
P1 P1
O4 O4
O3 O3
NAW NAW
CAT CAT
CBD CBD
CAB CAB
CBA CBA
OAH OAH
N N
CA CA
CB CB
C C
O O
NAD NAD
HAA1 HAA1
HAA2 HAA2
HAA3 HAA3
HBF HBF
HAR1 HAR1
HAR2 HAR2
HAU HAU
HAK HAK
HAP HAP
HAN HAN
HAM HAM
HAO HAO
HAQ HAQ
HAS1 HAS1
HAS2 HAS2
HBG HBG
HAW HAW
HAL HAL
HAT1 HAT1
HAT2 HAT2
HBD HBD
HAB1 HAB1
HAB2 HAB2
HAB3 HAB3
H H
HA HA
HB1C HB1C
HB2C HB2C
HB3C HB3C
HAD1 HAD1
HAD2 HAD2