Atom Nomenclature for 0H8

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 0H8

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
O2 O2
C2 C2
C3 C3
C4 C4
O4 O4
N N
CA CA
C C
O O
CB CB
CG1 CG1
CG2 CG2
N1 N1
CA1 CA1
C5 C5
O3 O3
CB1 CB1
CG CG
CD CD
N2 N2
CA2 CA2
P P
O1P O1P
O2P O2P
CB2 CB2
CG3 CG3
CD1 CD1
CE CE
NZ NZ
HO2 HO2
H21 H21
H22 H22
H31 H31
H32 H32
H H
HA HA
HB HB
HG11 HG11
HG12 HG12
HG13 HG13
HG21 HG21
HG22 HG22
HG23 HG23
HA1 HA1
HB2 HB2
HB3 HB3
HG2 HG2
HG3 HG3
HD2 HD2
HD3 HD3
HN2 HN2
HA2 HA2
HOP2 HOP2
HB1 HB1
HB21 HB21
HG1 HG1
HG24 HG24
HD1 HD1
HD21 HD21
HE1 HE1
HE2 HE2
HNZ1 HNZ1
HNZ2 HNZ2
O8 O8
H35 H35