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The systematic study of defects in the mineral structures is relevant not only in terms of basic problems of mineralogy, but reconstruction of evolution mineral-forming conditions. Despite numerous studies for structure defects in solids carried out in various scientific areas, there is no conventional approach to the description of relationships of types and concentrations of structure defects and physicochemical conditions of mineral-forming environment, stability during epigenetic transformation of minerals, and variability in the same minerals in rocks of different age and type. The electron spin resonance spectroscopy (ESR) allow for high precision and resolution study of point defects particularly in quartz, which is the most abundant mineral in the Earth crust. The aim of this study is to characterize paramagnetic centers in quartz from veins of the Kekura gold deposit, Western Chukotka, Russia. The deposit is spatially related to the Early Cretaceous granodiorite stock, which intrudes Upper Triassic flysch-like sequence. Mineralization in quartz veins and veinlets is represented by four mineralization stages: (1) cassiterite-scheelite-chalcopyrite-bismuth-arsenopyrite, (2) molybdenite, (3) gold with gold-bismuth tellurides and gold-scheelite substages, and (4) gold-silver-stibnite. The bulk of the economic mineralization (Stage 3) includes two substages. The first substage is represented by chalcopyrite III, high-fineness native gold (930–995), maldonite, aikinite, bismuth tellurides and sulfotellurides, bismuthinite. The second substage of Stage 3 mineralization is characterized by scheelite II, arsenopyrite III (S/As>1), pyrite, chalcopyrite IV, sphalerite I, galena I, tennantite-tetrahedrite II, native gold. The final mineralization stage, Stage 4, is characterized by stibnite, bournonite, boulangerite, high- and low-Ag tetrahedrite III, chalcopyrite V, Ag-Au and Au-Ag-Hg alloys with fineness 375-797, native silver, sphalerite II, galena-II, chalcostibite (?), acanthite