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We present the first structure of the active, triphosphate form of d4T (d4TTP) bound to a catalytic complex of HIV\u20101 RT\/dsDNA template\u2010primer. We also present a new strategy for disulfide (S\u2013S) chemical cross\u2010linking between N<jats:sup>6<\/jats:sup> of a modified adenine at the second overhang base to I63C in the fingers subdomain of RT. The cross\u2010link site is upstream of the duplex\u2010binding region of RT, however, the structure is very similar to published RT structures with cross\u2010linking to Q258C in the thumb, which suggests that cross\u2010linking at either site does not appreciably perturb the RT\/DNA structures. RT has a catalytic maximum at pH 7.5. We determined the X\u2010ray structures of the I63C\u2010RT\/dsDNA\/d4TTP cross\u2010linked complexes at pH 7, 7.5, 8, 8.5, 9, and 9.5. We found small (~0.5 \u00c5), pH\u2010dependent motions of the fingers subdomain that folds in to form the dNTP\u2010binding pocket. We propose that the pH\u2010activity profile of RT relates to this motion of the fingers. Due to side effects of neuropathy and lipodystrophy, use of d4T has been stopped in most countries, however, chemical modification of d4T might lead to the development of a new class of nucleoside analogs targeting RNA and DNA polymerases.<\/jats:p>","DOI":"10.1002\/pro.3559","type":"journal-article","created":{"date-parts":[[2018,11,30]],"date-time":"2018-11-30T08:05:36Z","timestamp":1543565136000},"page":"587-597","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Structure of HIV\u20101 reverse transcriptase\/d4TTP complex: Novel DNA cross\u2010linking site and pH\u2010dependent conformational changes"],"prefix":"10.1002","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5523-6940","authenticated-orcid":false,"given":"Sergio E.","family":"Martinez","sequence":"first","affiliation":[{"name":"Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology Rutgers University  Piscataway New Jersey 08854"},{"name":"Rega Institute for Medical Research and Department of Microbiology and Immunology  KU Leuven, Leuven 3000 Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph D.","family":"Bauman","sequence":"additional","affiliation":[{"name":"Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology Rutgers University  Piscataway New Jersey 08854"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8897-324X","authenticated-orcid":false,"given":"Kalyan","family":"Das","sequence":"additional","affiliation":[{"name":"Rega Institute for Medical Research and Department of Microbiology and Immunology  KU Leuven, Leuven 3000 Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eddy","family":"Arnold","sequence":"additional","affiliation":[{"name":"Center for Advanced Biotechnology and Medicine, and Department of Chemistry and 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