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There is an increasing number of PS I 3D structures deposited in the Protein Data Bank (PDB). The Triangular Spatial Relationship (TSR)-based algorithm converts 3D structures into integers (TSR keys). A comprehensive study was conducted, by taking advantage of the PS I 3D structures and the TSR-based algorithm, to answer three questions: (i) Are electron cofactors including P700, A<jats:sub>-1<\/jats:sub> and A<jats:sub>0<\/jats:sub>, which are chemically identical chlorophylls, structurally different? (ii) There are two electron transfer chains (A and B branches) in PS I. Are the cofactors on both branches structurally different? (iii) Are the amino acids in cofactor binding sites structurally different from those not in cofactor binding sites?<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The key contributions and important findings include: (i) a novel TSR-based method for representing 3D structures of pigments as well as for quantifying pigment structures was developed; (ii) the results revealed that the redox cofactor, P700, are structurally conserved and different from other redox factors. Similar situations were also observed for both A<jats:sub>-1<\/jats:sub> and A<jats:sub>0<\/jats:sub>; (iii) the results demonstrated structural differences between A and B branches for the redox cofactors P700, A<jats:sub>-1<\/jats:sub>, A<jats:sub>0<\/jats:sub> and A<jats:sub>1<\/jats:sub> as well as their cofactor binding sites; (iv) the tryptophan residues close to A<jats:sub>0<\/jats:sub> and A<jats:sub>1<\/jats:sub> are structurally conserved; (v) The TSR-based method outperforms the Root Mean Square Deviation (RMSD) and the Ultrafast Shape Recognition (USR) methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The structural analyses of redox cofactors and their binding sites provide a foundation for understanding the unique chemical and physical properties of each redox cofactor in PS I, which are essential for modulating the rate and direction of energy and electron transfers.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s12859-025-06038-y","type":"journal-article","created":{"date-parts":[[2025,1,14]],"date-time":"2025-01-14T08:26:01Z","timestamp":1736843161000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I"],"prefix":"10.1186","volume":"26","author":[{"given":"Lujun","family":"Luo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tarikul I.","family":"Milon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elijah K.","family":"Tandoh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter J.","family":"Galdamez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrei Y.","family":"Chistoserdov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianping","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Kern","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingchun","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wu","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,1,14]]},"reference":[{"key":"6038_CR1","doi-asserted-by":"publisher","first-page":"1703","DOI":"10.1126\/science.289.5485.1703","volume":"289","author":"DJ De Marais","year":"2000","unstructured":"De Marais DJ. 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