Atom Nomenclature for 2LM

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 2LM

Atom Name (V3) Atom Name (V2)
C C
N N
O1 O1
P P
N1 N1
C2 C2
C3 C3
O3 O3
C4 C4
C5 C5
C6 C6
CA CA
CB CB
SD SD
CE CE
CG CG
C2A C2A
C4A C4A
C5A C5A
OP1 OP1
OP2 OP2
OP3 OP3
OP4 OP4
O2 O2
HO3 HO3
H6 H6
HB HB
HBA HBA
HE HE
HEA HEA
HEB HEB
HG HG
HGA HGA
H2A H2A
H2A1 H2A1
H2A2 H2A2
H4A H4A
H5A H5A
H5A1 H5A1
HOP2 HOP2
HOP3 HOP3
H4A1 H4A1
H2 H2