{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T05:51:36Z","timestamp":1760853096989},"reference-count":44,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2004,2,3]],"date-time":"2004-02-03T00:00:00Z","timestamp":1075766400000},"content-version":"vor","delay-in-days":4203,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[1992,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The conformation of the staphylococcal nuclease\u2010bound metal\u2013dTdA complex, previously determined by NMR methods [Weber, D.J., Mullen, G.P., Mildvan, A.S. (1991) Biochemistry 30:7425\u20137437] was docked into the X\u2010ray structure of the enzyme\u2013Ca<jats:sup>2+<\/jats:sup>\u20103\u2032,5\u2032\u2010pdTp complex [Loll, P.J., Lattman, E.E. (1989) Proteins: Struct., Funct., Genet. 5:183\u2013201] by superimposing the metal ions, taking into account intermolecular nuclear Overhauser effects from assigned aromatic proton resonances of Tyr\u201085, Tyr\u2010113, and Tyr\u2010115 to proton resonances of the leaving dA moiety of dTdA, and energy minimization to relieve small overlaps. The proton resonances of the Phe, Tyr, and Trp residues of the enzyme in the ternary enzyme\u2013La<jats:sup>3+<\/jats:sup>\u2010dTdA complex were sequence specifically assigned by 2D phase\u2010sensitive NOESY, with and without deuteration of the aromatic protons of the Tyr residues, and by 2D heteronu\u2010clear multiple quantum correlation (HMQC) spectroscopy and 3D NOESY\u2010HMQC spectros\u2010copy with <jats:sup>15<\/jats:sup>N labeling. While resonances of most Phe, Tyr and Trp residues were unshifted by the substrate dTdA from those found in the enzyme\u2013La<jats:sup>3+<\/jats:sup>\u20133\u2032,5\u2032\u2010pdTp complex and the enzyme\u2013Ca<jats:sup>2+<\/jats:sup>\u20133\u2032,5\u2032\u2010pdTp complex, proton resonances of Tyr\u201085, Tyr\u2010113, Tyr\u2010115, and Phe\u201034 were shifted by 0.08 to 0.33 ppm and the <jats:sup>15<\/jats:sup>N resonance of Tyr\u2010113 was shifted by 2.1 ppm by the presence of substrate. The optimized position of enzyme\u2010bound dTdA shows the 5\u2032\u2010dA leaving group to partially overlap the inhibitor, 3\u2032,5\u2032\u2010pdTp (in the X\u2010ray structure). Tne 3\u2032\u2010TMP moiety of dTdA points toward the solvent in a channel defined by Ile\u201018, Asp\u201019, Thr\u201022, Lys\u201045, and His\u201046. The phosphate of dTdA is coordinated by the metal, and an adjacent inner sphere water ligand is positioned to donate a hydrogen bond to the general base Glu\u201043 and to attack the phosphorus with inversion. Arg\u201035 and Arg\u201087 donate monodentate hydrogen bonds to different phosphate oxygens of dTdA, with Arg\u201087 positioned to protonate the leaving 5\u2032\u2010oxygen of dA, thus clarifying the mechanism of hydrolysis. Model building of an additional 5\u2032\u2010dGMP onto the 3\u2032\u2010oxygen of dA placed this third nucleotide onto a surface cleft near residues Glu\u201080, Asp\u201083, Lys\u201084, and Tyr\u2010115 with its 3\u2032\u2010OH group accessible to the solvent, thus defining the size of the substrate binding site as accommodating a trinucleotide. \u00a9 1992 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.340130402","type":"journal-article","created":{"date-parts":[[2005,5,29]],"date-time":"2005-05-29T01:19:35Z","timestamp":1117329575000},"page":"275-287","source":"Crossref","is-referenced-by-count":54,"title":["NMR docking of a substrate into the X\u2010ray structure of staphylococcal nuclease"],"prefix":"10.1002","volume":"13","author":[{"given":"David J.","family":"Weber","sequence":"first","affiliation":[]},{"given":"Apostolos G.","family":"Gittis","sequence":"additional","affiliation":[]},{"given":"Gregory P.","family":"Mullen","sequence":"additional","affiliation":[]},{"given":"Chitrananda","family":"Abeygunawardana","sequence":"additional","affiliation":[]},{"given":"Eaton E.","family":"Lattman","sequence":"additional","affiliation":[]},{"given":"Albert S.","family":"Mildvan","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2004,2,3]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00226229"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.76.6.2551"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340050302"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00439a028"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00453a011"},{"key":"e_1_2_1_7_2","first-page":"309","volume-title":"Metal Ions in Biological Systems.","author":"Mildvan A. 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