Recently I was surprised by some cases of nucleotides with missing atoms in PDB entry 1pns. The story started like this: 3DNA/DSSR maps various nucleotide names to one-letter codes, based on the data file baselist.dat (see post Modified nucleotides in the PDB). In the meantime, 3DNA/DSSR internally assigns a nucleotide as either purine or pyrimidine, by virtue of coordinates of base atoms. Be definition, purines should only include A/a/G/g/I/i, and pyrimidines C/c/T/t/U/u/P/p. However, no consistency check has been implemented in DSSR until just now.

I first noticed the inconsistency between residue name and atom coordinates for nucleotide A6 on chain U (hereafter referred to as U.A6) in 1pns. The nucleotide has standard name ‘  A’, obviously a purine. However, somehow DSSR classified it as a pyrimidine based on atomic coordinates. Upon further check of the PDB data file, I found the following remarks:

REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;            
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470       A U   6    N9   C8   N7                                        
REMARK 470       G U   8    N9   C8   N7                                        
REMARK 470       A U  12    N9   C8   N7                                        
REMARK 470       A U  13    N9   C8   N7                                        
REMARK 470       A U  14    N9   C8   N7                                        

The atomic coordinates for U.A6 are as below:

ATOM  34447  P     A U   6      81.861  37.210  78.651  1.00378.87           P  
ATOM  34448  OP1   A U   6      80.631  37.121  77.831  1.00378.87           O  
ATOM  34449  OP2   A U   6      81.665  37.221  80.119  1.00378.87           O  
ATOM  34450  O5'   A U   6      82.707  38.495  78.212  1.00378.87           O  
ATOM  34451  C5'   A U   6      83.948  38.777  78.887  1.00378.87           C  
ATOM  34452  C4'   A U   6      84.600  40.000  78.276  1.00378.87           C  
ATOM  34453  O4'   A U   6      84.975  39.698  76.901  1.00378.87           O  
ATOM  34454  C3'   A U   6      83.714  41.239  78.153  1.00378.87           C  
ATOM  34455  O3'   A U   6      83.654  41.968  79.369  1.00378.87           O  
ATOM  34456  C2'   A U   6      84.403  42.015  77.020  1.00378.87           C  
ATOM  34457  O2'   A U   6      85.564  42.655  77.474  1.00378.87           O  
ATOM  34458  C1'   A U   6      84.834  40.864  76.105  1.00378.87           C  
ATOM  34459  C5    A U   6      82.033  39.296  74.209  1.00378.87           C  
ATOM  34460  C6    A U   6      82.941  39.553  75.166  1.00378.87           C  
ATOM  34461  N6    A U   6      81.170  39.949  72.090  1.00378.87           N  
ATOM  34462  N1    A U   6      83.830  40.588  75.041  1.00378.87           N  
ATOM  34463  C2    A U   6      83.843  41.410  73.939  1.00378.87           C  
ATOM  34464  N3    A U   6      82.899  41.124  72.974  1.00378.87           N  
ATOM  34465  C4    A U   6      81.968  40.108  73.016  1.00378.87           C  

No atom records for N7, C8 and N9. So far, so good. However, surprise came when I visualized U.A6 in Jmol, as shown in the following image. Note here atom N1 is connected to C1’ as in pyrimidines, and N6 is bonded to C4!

The same issue also exists for U.G8 (see figure below), U.A12, U.A13, and U.A14.

It is beyond my imagination to understand why such weird cases exist in the PDB, even given the lousy resolution (8.7 Å) of 1pns.