# The following list gives the correspondence between a uncommon base with # its canonical counterparts: A, C, G, I, T and U. It is based on an # analysis of all the NDB entries and a careful check of each residue given # here, and is intended to make analyzing nucleic acid structures with # unusual base residues easier. # New base residues can be added to this list following the same format. # The format of this list is: three-letter residue name as in a PDB file # followed by a one-letter, one line per pair. Those with less the # three-letter will be prepended with space. For each base X here, there are # should be a file name Atomic_X.pdb in your current directory or $X3DNA. # An empty line or a line STARTING with # is a comment. # common residues: in upper case A A ADE A DA A DA5 A DA3 A RA A RA5 A RA3 A C C CYT C DC C DC5 C DC3 C RC C RC5 C RC3 C G G GUA G DG G DG5 G DG3 G RG G RG5 G RG3 G I I INO I T T THY T DT T DT5 T DT3 T U U URA U RU U RU5 U RU3 U # The rare PSU in RNA is named P, and there is a Atomic_P.pdb file. PSU P # C1* connected to C5 instead of N1 # This following list is in alphabetical order and in lower case N u S t # S4 connected to C4 +A a +C c +G g +I i +T t +U u PU a # Two C connected to N6 YG g # C3 to N3, C11/C12 to N2/N1 to form a 5-member ring 1AP g # N6 not O6 1MA a # C connected to N1 1MG g # C connected to N1 2DA a 2DT t 2MA a # C connected to C2 2MG g # C connected to N2 4SC c # S4* instead of O4* for the sugar, C to C5 4SU u # S4 instead O4 of connected to C4 5IU u # I connected to C5 5MC c # C connected to C5 5MU u # C connected to C5, could be T 5NC c # N5 instead of C5 in the ring 6MP a 7MG g # C connected to N7 A23 a AD2 a AET a # C/CON connected to N6 AMD a AMP a APN a ATP a AZT t CCC c CMP a CPN c DAD a DCT c DDG g DG3 g DHU u # non-planar DOC c EDA a # C10/C11 connected to N1/N6 to form a 5-member ring G7M g # C connected to N7 GDP g GNP g GPN g GTP g GUN g H2U u # non-planar HPA a IPN t # I connected to C5 M2G g # Two Cs connected to N2 MGT g # C connected to N7 MIA a # S connected to C2, C to N6 OMC c OMG g OMU u ONE u # No O2 atom P2U p # C1* connected to C5 instead of N1 PGP g PPU a # Two Cs connected to N6 PRN a # No N6 atom PST t QSI a QUO g # C7 instead of N7 RIA a SAH a SAM a T23 t T6A a # C connected to N6 TAF t TLC t TPN t TSP t TTP t UCP u VAA a YYG g # C11/C12 connected to N1/N1 to form a 5-member ring 70U u # tr0003 12A a 2MU u 127 u # ad0011 125 u # ad0012 126 u # ad0014 MEP u # ad0013 TLN u # ad0020 ADP a # pd0181 TTE t # pd0196 PYO u # pr0040: missing O4 SUR u # pr0043: O2 to S2 PSD a # pr0057 S4U u # pr0059: O4 to S4 CP1 c # up0001 TP1 t # up0001 NEA a # pd0188 GCK c # ad0025 CH c # pdb1kos EDC g # pdb1b60 ======> not a common base> judged as Y DFC c # pdb1fv7 DFG g # pdb1fv7 DRT t # pdb1fv8 2AR a # pdb1fyi 8OG g # pdb1fyi IG g # pdb1g3a: swap N2 and O6 IC c # pdb1g3a: swap O2 and N4 IGU g # pdb1be5 IMC c # pdb1be5 GAO g # pdb1ho6 UAR u # pdb1ho6 CAR c # pdb1ho6 PPZ a # pdb1i5v M1G g # pdb1k29 ABR a # pdb1k5e ABS a # pdb1k5f S6G g # pdb1kb1 HEU u # pdb1kxs P g # pdb1lae DNR c # pdb1laq MCY c # pdb1a83 TCP t # pdb1ac3 LGP g # pdb1ac9 GSR g # pdb1af1 X g # pdb1ag5 R a # pdb1agk Y a # pdb1ago E a # pdb1agu GSS g # pdb1ap1 THX t # pdb1aul 6CT t # pdb1dau TEP g # pdb1eht GN7 g # pdb1gn7 FAG g # pdb1hm1 PDU u # pdb1p3x MA6 a # pdb1wts UMP u # pdb229d SC c # pdb8psh GS g # pdb8psh TS t # pdb8psh AS a # pdb8psh ATD t # pdb1bx5 T3P t # pdb1c2q 5AT t # pdb1c95 MMT t # pdb1cx5 SRA a # pdb1d0t 6HG g # pdb1ejz 6HC c # pdb1ejz 6HT t # pdb1ejz 6HA a # pdb1ejz 55C c # pdb1el2 U8U u # pdb1fl8 BRO u # pdb344d BRU u # pdb1cs7 5IT u # pdb1a6y ADI a # pdb1jx4 5CM c # pdb1bsu IMP g # pdb1bsu THM t # pdb1mht URI u # pdb1i5l AMO a # pdb1il2 FHU p # pdb1k8w: C1' connected to C5, not N1 TSB a # pdb1kog CMR c # 1k1r RMP a # 1k1r SMP a # 1k1h