Atom Nomenclature for 0GM

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 0GM

Atom Name (V3) Atom Name (V2)
C C
O O
CA CA
CB1 CB1
C1A C1A
C2A C2A
C3A C3A
C4A C4A
C11 C11
C5A C5A
C6A C6A
C7A C7A
C8A C8A
C12 C12
CB2 CB2
C1B C1B
C2B C2B
C3B C3B
C4B C4B
C13 C13
C5B C5B
C6B C6B
C7B C7B
C8B C8B
C14 C14
N N
CA1 CA1
C1 C1
O1 O1
CB CB
CG CG
CD CD
OE1 OE1
N1 N1
CA2 CA2
CB3 CB3
CG1 CG1
CD1 CD1
CD2 CD2
CH CH
OH OH
CM CM
C2 C2
O2 O2
N2 N2
CA3 CA3
C3 C3
O3 O3
CB4 CB4
CG2 CG2
CD3 CD3
CD4 CD4
N3 N3
CA4 CA4
CG3 CG3
CD5 CD5
CD6 CD6
CE1 CE1
CE2 CE2
CZ CZ
CB5 CB5
N4 N4
HA HA
HB1 HB1
HB1A HB1A
H2A H2A
H3A H3A
H4A H4A
H5A H5A
H6A H6A
H7A H7A
H8A H8A
HB2 HB2
HB2A HB2A
H2B H2B
H3B H3B
H4B H4B
H5B H5B
H6B H6B
H7B H7B
H8B H8B
HN HN
HA1 HA1
HB HB
HBA HBA
HG HG
HGA HGA
HN1 HN1
HA2 HA2
HB3 HB3
HB3A HB3A
HG1 HG1
HD1 HD1
HD1A HD1A
HD1B HD1B
HD2 HD2
HD2A HD2A
HD2B HD2B
HH HH
HOH HOH
HM HM
HMA HMA
HN2 HN2
HA3 HA3
HB4 HB4
HB4A HB4A
H17 H17
HD3 HD3
HD3A HD3A
H13 H13
HD4 HD4
HD4A HD4A
HD4B HD4B
HN3 HN3
HA4 HA4
HA4A HA4A
HD5 HD5
HD6 HD6
HE2 HE2
HZ HZ
HB5 HB5
HB5A HB5A
HN4 HN4