Atom Nomenclature for UC1

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 UC1

Atom Name (V3) Atom Name (V2)
C2 C2
C4 C4
C5 C5
C6 C6
O7 O7
C8 C8
C9 C9
C10 C10
C11 C11
CA CA
C C
S S
N N
C1 C1
C3 C3
CL CL
OB OB
CC CC
CD CD
CE CE
CF CF
CG CG
H2 H2
H5 H5
H6 H6
H10 H10
H11 H11
HA1 1HA
HA2 2HA
HA3 3HA
HN HN
HC1 1HC
HC2 2HC
HD HD
HF1 1HF
HF2 2HF
HF3 3HF
HG1 1HG
HG2 2HG
HG3 3HG