Atom Nomenclature for 0EK

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 0EK

Atom Name (V3) Atom Name (V2)
O1 O1
C C1
O2 O2
CT C2
C1 C3
C2 C4
C3 C5
N N1
CA C6
C4 C7
O O4
CB C8
CG C9
CD1 C10
CD2 C11
CE1 C12
CE2 C13
CZ C14
N1 N2
CA1 C15
C5 C16
O3 O6
CB1 C17
CG1 C18
ND1 N3
CD21 C19
CE11 C20
NE2 N4
N2 N5
CA2 C21
CB2 C22
CG2 C23
CD11 C24
CD22 C25
CE12 C26
CE21 C27
CZ1 C28
CH C29
OH O8
CM C30
N11 N6
CB21 C31
CG21 C32
CD3 C33
CD4 C34
C6 C35
O4 O9
N3 N7
CA3 C36
C7 C37
O5 O11
CB3 C38
CG3 C39
CD C40
CE C41
NZ N8
N4 N9
CA4 C42
C8 C43
O6 O13
CB4 C44
CG4 C45
CD12 C46
CD23 C47
CE13 C48
CE22 C49
CZ2 C50
OXT O14
H11 H1
H12 H2
H13 H3
H21 H4
H22 H5
H23 H6
H31 H7
H32 H8
H33 H9
H H11
HA H13
HB2 H14
HB3 H15
HD1 H16
HD2 H17
HE1 H18
HE2 H19
HZ H20
H1 H22
HA1 H24
HB21 H25
HB31 H26
HD11 H27
HD21 H28
HE11 H29
HE21 H30
H2 H32
HA2 H34
HB22 H35
HB32 H36
HG H37
HD12 H38
HD13 H39
HD23 H40
HD22 H41
HE12 H42
HE13 H43
HE23 H44
HE22 H45
HZ2 H46
HZ3 H47
HH H48
HO H49
HM1 H50
HM2 H51
HB23 H52
HB24 H53
HG2 H54
HD31 H55
HD32 H56
HD33 H57
HD41 H58
HD42 H59
HD43 H60
H3 H62
HA3 H64
HB25 H65
HB33 H66
HG21 H67
HG3 H68
HD24 H69
HD3 H70
HE24 H71
HE3 H72
HZ1 H73
HZ21 H74
HZ31 H75
H4 H77
HA4 H79
HB26 H80
HB34 H81
HD14 H82
HD25 H83
HE14 H84
HE25 H85
HZ4 H86
HXT H87