Boğdan Palace
From Byzantine Topographic Studies by Paspates (1877)
Boğdan Sarayı (“Moldavian Palace”) is located in the northwestern part of the city near Kefeli Mosque. It is a Palaiologan structure, perhaps dating to the 14th century. While it has been identified as the Church of St. John the Baptist in Petra, its originally dedication is unknown.
The building was a single-nave structure with two stories, measuring approximately 9 by 4 meters. Its masonry consists of alternating bands of ashlar and bricks, typical of Palaiologan construction. While the typical medieval Byzantine church had a tripartite sanctuary, it has a single apse that pointed to the north. Three sarcophagi discovered under the floor of the lower level suggest that it was funerary chapel. Its shallow dome, recorded in early photographs, was a post-Byzantine modification. It is possible that it originally had a wooden roof.
Its current name derives from the fact that in the early sixteenth century the chapel was part of the Moldavian (Turkish “Boğdan”) embassy to the Sublime Porte and was dedicated to Saint Nicholas. It was damaged by fire in 1784 and fell into ruin during the 19th century.
From the Nicholas V. Artamonoff Collection
Apse Ruins

Plan by Van Millingen (1912)
Apse Ruins

Sources
Architecture and Ritual in the Churches of Constantinople Ninth to Fifteenth Centuries by Vasileios Marinis
Bildlexikon zur Topographie Istanbuls: Byzantion, Konstantinupolis, Istanbul by Wolfgang Müller-Wiener
Boğdan Sarayı (Encyclopaedia of the Hellenic World)
Resources
Byzantine Churches of Constantinople Photo Album (Byzantine Legacy Flickr)