[phenixbb] modified nucleotide not linked

tuske at cabm.rutgers.edu tuske at cabm.rutgers.edu
Fri Mar 25 15:02:14 PDT 2011

Hello all,

I am refining three protein-DNA complexes each with a different modified
nucleotide-monophosphate residue at the 3'-terminus of its DNA strand. 
Two of these worked fine after sending the pdb file through ready-set. 
With the third structure the modified nucleoside-monophosphate residue is
not recognized as linked to the previous nucleotide-monophospahe--no
phosphodiester bond formation.

The only difference between the two that "worked" and the one that didn't
is the nature of the deoxyribose sugar modification.  The first two have
substituents at the 4'-carbon of the deoxyribose sugar, the third has the
4'-oxygen of the deoxyribose sugar substituted with a -CH2- making it a
cylcopentyl pseudo-sugar.

The bond lengths and angles are reasonable in the starting model, I had no
problem doing the initial refinement in CNS after defining topology and
parameter files.

The output for this in the log file is:
Chain: "P"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 439
          Unusual residues: {'CAR': 1}
          Classifications: {'undetermined': 1, 'DNA': 20}
          Modifications used: {'5*END': 1}
          Link IDs: {None: 1, 'rna3p': 19}
            Not linked:
              pdbres="CYT P 821 " segid="P   "
              pdbres="CAR P 822 " segid="P   "



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