Atom Nomenclature for RO0

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 RO0

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
N8 N8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
O14 O14
N15 N15
O16 O16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
O28 O28
C29 C29
O30 O30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
O37 O37
C38 C38
C39 C39
C40 C40
H4 H4
H6 H6
H71 1H7
H72 2H7
H10 H10
H111 1H11
H112 2H11
H17 H17
H18 H18
H191 1H19
H192 2H19
H193 3H19
H201 1H20
H202 2H20
H211 1H21
H212 2H21
H221 1H22
H222 2H22
H223 3H22
H24 H24
H251 1H25
H252 2H25
H261 1H26
H262 2H26
H29 H29
H311 1H31
H312 2H31
H313 3H31
H331 1H33
H332 2H33
H333 3H33
H35 H35
H36 H36
H38 H38
H39 H39
H401 1H40
H402 2H40
H403 3H40