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Figure 2 | BMC Bioinformatics

Figure 2

From: Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate

Figure 2

NAD molecules from X-ray crystal structure 2OHX. For comparison purposes, one molecule is superimposed on the other and then offset slightly. The atom names are similarly offset for the diastereotopic oxygen atoms of the adenine-side phosphate group. Note the differences in names for the pro-R and pro-S atoms. Both molecules of NAD shown are from an alcohol dehydrogenase structure [PDB:2OHX][16]. Following the CIP-algorithm, since all four oxygen atoms have the same atomic number, their priority is determined by subsequent bonded groups. The O3 oxygen atom is bonded to the next phosphorus atom and the O5' oxygen atom is bonded to the preceding C5' carbon atom, while the remaining two oxygen atoms are unbonded except to the original phosphorus atom. Therefore, the O3 oxygen atom has the highest priority, the O5' oxygen atom has the second highest priority, and the remaining two oxygen atoms tie for the lowest priority. The pro-S atom is the one that, if it were replaced with an atom of highest priority, would make the phosphorus atom chiral with an S configuration. Both molecules are drawn using red for oxygen, blue for nitrogen, and orange for phosphorus. One is drawn using light blue for carbon and the other is drawn using white for carbon.

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