Atom Nomenclature for SPN

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 SPN

Atom Name (V3) Atom Name (V2)
CMA CMA
O1 O1
CM1 CM1
CM2 CM2
C1 C1
C2 C2
O2 O2
C3 C3
C4 C4
C5 C5
CM3 CM3
C6 C6
C7 C7
C8 C8
C9 C9
CM4 CM4
C10 C10
C11 C11
C12 C12
C13 C13
CM5 CM5
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
CM6 CM6
C19 C19
C20 C20
C21 C21
C22 C22
CM7 CM7
C23 C23
C24 C24
C25 C25
C26 C26
CM8 CM8
C27 C27
C28 C28
C29 C29
C30 C30
CM9 CM9
CMB CMB
HMA1 1HMA
HMA2 2HMA
HMA3 3HMA
HM11 1HM1
HM12 2HM1
HM13 3HM1
HM21 1HM2
HM22 2HM2
HM23 3HM2
H31 1H3
H32 2H3
H4 H4
HM31 1HM3
HM32 2HM3
HM33 3HM3
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H8 H8
HM41 1HM4
HM42 2HM4
HM43 3HM4
H101 1H10
H102 2H10
H111 1H11
H112 2H11
H12 H12
HM51 1HM5
HM52 2HM5
HM53 3HM5
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
HM61 1HM6
HM62 2HM6
HM63 3HM6
H19 H19
H201 1H20
H202 2H20
H211 1H21
H212 2H21
H22 H22
HM71 1HM7
HM72 2HM7
HM73 3HM7
H231 1H23
H232 2H23
H241 1H24
H242 2H24
H25 H25
HM81 1HM8
HM82 2HM8
HM83 3HM8
H271 1H27
H272 2H27
H281 1H28
H282 2H28
H29 H29
HM91 1HM9
HM92 2HM9
HM93 3HM9
HMB1 1HMB
HMB2 2HMB
HMB3 3HMB