Seven carotenoid molecules were found in the 3.5 À structure, whereas 11 were identified in the 3.0 À structure; all of these carotenoids have an all-trans configuration. These numbers are lower compared to the 22 carotenoids found in cyano-bacterial PSI , which probably coincides with the lower number of Chls in PSII than in PSI (96 Chls were found in PSI, ). Among the 11 carotenoids in PSII, 3 are located in CP43, 5 in CP47, 1 in a space surrounded by CP43 and PsbJ, PsbK, PsbZ, and X1, and one each in D1 and D2. Four of the five carotenoids in CP47 are clustered in the monomer-monomer interface, whereas other carotenoids are located at the periphery of PSII. Almost all of these carotenoids are in close contact with Chl a molecules, making them capable of rapidly transferring excitation energy to the nearby Chl a molecules, as well as quenching the triplet state of Chl a in order to protect PSII from excessive light-induced damage.
The two carotenoids associated with PSII-RC have special functions, one associated with D1 and the other one with D2. Their presence in the isolated D1/D2-RC complex has been reported earlier from biochemical  and various spectroscopic studies [63-65]. CarD2 is located close to ChlZD2 and Cyt b559 with an orientation approximately parallel to the membrane, resulting in a distance of 6.8 À between CarD2-ChlZD2, 11.7À between Carra-Cyt b559, and 13.2À between Carra- ChlD2 at the closest positions of each molecule pair (Figure 4.3a). These distances suggest that CarD2 is capable of mediating electron transfer from ChlZD2 and Cyt b559 to the PSII-RC, a path that has been designated as secondary, or side electron transfer reactions which operates when the Mn4Ca cluster is not functional, such as at low temperature [64, 66, 67]. This side reaction may also become important in protecting the PSII-RC from photo-damage under strong light illumination where electron donation from the Mn4Ca may not be rapid enough to compensate for the charge generated at RC. On the other hand, CarD1 is located close to ChlZD1 with an orientation nearly perpendicular to the membrane plane. The distance between CarD1-ChlZD1 is 4.1 A, and that between CarD1-ChlD1 is 19.9 A, at their closest positions (Figure 4.3a). The longer distance between CarD1 and the RC-Chl suggests that this carotenoid is not efficient in mediating the possible secondary electron transfer from ChlZD1 to RC; the close location of CarD1 with ChlZD1 suggests that it is optimized for quenching the ChlZD1 triplet state as well as singlet oxygen that could be produced by the triplet state of RC (3P680) . Indeed, CarD1 is in close position with a cluster of four carotenoids associated with CP47 in the neighboring monomer, which is then connected to the bulk Chl a of CP47, supporting the role of CarD1 as an energy quencher [12, 68]. Also in agreement with this is the slightly higher redox potential of CarD1 than CarD2 . calculated from the current structure  , making CarD2 a preferential carrier mediating electron transfer from ChlZD2 and/or Cyt b559 to PSII - RC. The preferential location of the secondary electron transfer pathway on the D2 side involving Cyt b559 and ChlZD2 has been reported based on spectroscopic as well as mutagenesis studies. Some earlier reports, however, also suggested the involvement of ChlZD1 at the D1 side in the secondary electron transfer reactions (for review, see  ).
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