Fig. 3
Hierarchical cluster analysis of electron cofactors P700, A−1, A0 and connecting chlorophyll molecules demonstrating the capacity of the TSR algorithm, which can distinguish their 3D structural differences. Panel a, the hierarchical cluster analysis of 3D structural relationships between P700, A−1, A0 and connecting chlorophyll molecules. ACA (ACB) represents the connecting chlorophyll molecule on the PsaA (PsaB) side; panel b, the side-by-side structural comparisons between one type of cofactor pairs and between that type of cofactor and other types of cofactor pairs. The average similarity values, SDs, and 25/75 percentiles are indicated. *** means a p value is less than 0.001 using a t-test; panel c, the Venn diagram showing the numbers of TSR keys exclusively belonging to each type of cofactor class (the P700 cofactor class, A−1 cofactor class, A0 cofactor class and the connecting chlorophyll (AC) class), and the regions between any two, three and four cofactor classes; panels d and e, one A0 specific TSR key (669744562). The triangle corresponding to this key is constructed from three atoms (C1, NB and NC) of A0A and is shown in panel (d), and the triangle corresponding to the key 669,744,562 constructed from three atoms (C1, NA and NC or C6, NA and ND) of A0B is shown in panel (e). The PDB ID is labeled