Atom Nomenclature for ERY

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 ERY

Atom Name (V3) Atom Name (V2)
C10 C10
C11 C11
C12 C12
C13 C13
O2 O2
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
O11 O11
C1 C1
O1 O1
O3 O3
O7 O7
C34 C34
C33 C33
C35 C35
O12 O12
O13 O13
C36 C36
C30 C30
C32 C32
O10 O10
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
O9 O9
N1 N1
C27 C27
O8 O8
C28 C28
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
O4 O4
O5 O5
O6 O6
C20 C20
C29 C29
C21 C21
C37 C37
C31 C31
C19 C19
H10 H10
H11 H11
H13 H13
H2 H2
H3 H3
H4 H4
H5 H5
H71 1H7
H72 2H7
H8 H8
H341 1H34
H342 2H34
H343 3H34
H331 1H33
H332 2H33
H333 3H33
H351 1H35
H352 2H35
H353 3H35
HO12 HO12
HO13 HO13
H361 1H36
H362 2H36
H301 1H30
H302 2H30
H303 3H30
H321 1H32
H322 2H32
H323 3H32
HO10 HO10
H22 H22
H23 H23
H24 H24
H251 1H25
H252 2H25
H26 H26
H271 1H27
H272 2H27
H273 3H27
HO8 HO8
H281 1H28
H282 2H28
H283 3H28
H14 H14
H151 1H15
H152 2H15
H17 H17
H18 H18
HO6 HO6
H201 1H20
H202 2H20
H203 3H20
H291 1H29
H292 2H29
H293 3H29
H211 1H21
H212 2H21
H213 3H21
H371 1H37
H372 2H37
H373 3H37
H311 1H31
H312 2H31
H313 3H31
H191 1H19
H192 2H19
H193 3H19