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A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry

Table 1. Cartesian coordinates of non-hydrogen atoms in the standard reference frames of the five common nitrogenous bases

 


           Atom  Base         x(Å)  y(Å)  z(Å)

Adenine


ATOM      1  C1'   A A   1      -2.479   5.346   0.000

ATOM      2  N9    A A   1      -1.291   4.498   0.000

ATOM      3  C8    A A   1       0.024   4.897   0.000

ATOM      4  N7    A A   1       0.877   3.902   0.000

ATOM      5  C5    A A   1       0.071   2.771   0.000

ATOM      6  C6    A A   1       0.369   1.398   0.000

ATOM      7  N6    A A   1       1.611   0.909   0.000

ATOM      8  N1    A A   1      -0.668   0.532   0.000

ATOM      9  C2    A A   1      -1.912   1.023   0.000

ATOM     10  N3    A A   1      -2.320   2.290   0.000

ATOM     11  C4    A A   1      -1.267   3.124   0.000

END

					

Cytosine


ATOM      1  C1'   C A   1      -2.477   5.402   0.000

ATOM      2  N1    C A   1      -1.285   4.542   0.000

ATOM      3  C2    C A   1      -1.472   3.158   0.000

ATOM      4  O2    C A   1      -2.628   2.709   0.001

ATOM      5  N3    C A   1      -0.391   2.344   0.000

ATOM      6  C4    C A   1       0.837   2.868   0.000

ATOM      7  N4    C A   1       1.875   2.027   0.001

ATOM      8  C5    C A   1       1.056   4.275   0.000

ATOM      9  C6    C A   1      -0.023   5.068   0.000

END

					

Guanine


ATOM      1  C1'   G A   1      -2.477   5.399   0.000

ATOM      2  N9    G A   1      -1.289   4.551   0.000

ATOM      3  C8    G A   1       0.023   4.962   0.000

ATOM      4  N7    G A   1       0.870   3.969   0.000

ATOM      5  C5    G A   1       0.071   2.833   0.000

ATOM      6  C6    G A   1       0.424   1.460   0.000

ATOM      7  O6    G A   1       1.554   0.955   0.000

ATOM      8  N1    G A   1      -0.700   0.641   0.000

ATOM      9  C2    G A   1      -1.999   1.087   0.000

ATOM     10  N2    G A   1      -2.949   0.139  -0.001

ATOM     11  N3    G A   1      -2.342   2.364   0.001

ATOM     12  C4    G A   1      -1.265   3.177   0.000

END

					

Thymine


ATOM      1  C1'   T A   1      -2.481   5.354   0.000

ATOM      2  N1    T A   1      -1.284   4.500   0.000

ATOM      3  C2    T A   1      -1.462   3.135   0.000

ATOM      4  O2    T A   1      -2.562   2.608   0.000

ATOM      5  N3    T A   1      -0.298   2.407   0.000

ATOM      6  C4    T A   1       0.994   2.897   0.000

ATOM      7  O4    T A   1       1.944   2.119   0.000

ATOM      8  C5    T A   1       1.106   4.338   0.000

ATOM      9  C5M   T A   1       2.466   4.961   0.001

ATOM     10  C6    T A   1      -0.024   5.057   0.000

END

					

Uracil


ATOM      1  C1'   U A   1      -2.481   5.354   0.000

ATOM      2  N1    U A   1      -1.284   4.500   0.000

ATOM      3  C2    U A   1      -1.462   3.131   0.000

ATOM      4  O2    U A   1      -2.563   2.608   0.000

ATOM      5  N3    U A   1      -0.302   2.397   0.000

ATOM      6  C4    U A   1       0.989   2.884   0.000

ATOM      7  O4    U A   1       1.935   2.094  -0.001

ATOM      8  C5    U A   1       1.089   4.311   0.000

ATOM      9  C6    U A   1      -0.024   5.053   0.000

END

					

* Standard chemical structures taken from Clowney et al. [5]. These data do not include C1' atoms, which are placed here in the least-squares plane of the base atoms, with the purine C1'–N9 bond length and C1'–N9–C4 valence angle set respectively to 1.46 Å and 126.5° and the pyrimidine C1'–N1 bond and C1'–N1–C2 angle to 1.47 Å and 118.1°. These distances and angles are based on the average glycosyl geometries of purines and pyrimidines in high resolution crystal structures of nucleic acid analogs from the Cambridge Structure Database (J. Westbrook and H. M. Berman, unpublished data).

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