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Ernst Eduard Kummer was buried in the St. Jacobi Kirchhof:
Finally, on May 14, 1893, influenza swept him away in the midst of his loved ones. On a glorious sunny day in May, his mortal remains were lowered into the tomb in the Jacobikirchhof, around which all those who held him dear had gathered.
— Vorstand der Berliner Mathematische Gesellschaft (eds): "Festschrift zur Feier des 100. Geburtstages Eduard Kummers; mit Briefen an seine Mutter und an Leopold Kronecker", B.G. Teubner: Leipzig, 1910. (p36, translated from German)
In lists about 'famous persons buried there', Kummer usually does not feature a spot.
Since the cemetery is located some distance from its church, another snippet from a obituary might give a clue as to why:
On a beautiful sunny May day, when the lilacs were fragrant and the songbirds were rejoicing, his earthly remains were lowered into the tomb in the Jacobikirchhof near the Rollkruge, around which all had gathered who held him dear and worthy, and over which the wreathed flag of the mathematical society of the University of Berlin, which he had favored from its founding, was lowered.
— E. Lampe: "Nachruf für Ernst Eduard Kummer", Jahresbericht der Deutschen Mathematiker-Vereinigung 3, 13-28 (1892-1893), quoted from: Andre Weil (ed): "Ernst Eduard Kummer Collected Papers. Volume I. Contributions to Number Theory", Springer: Berlin, Heidelberg, New York, 1975. (p21) (Same text as in this scan)
The Rollkrug was a now demolished tavern and the cemetery was made smaller a few times, especially for building a subway and roads, demolishing quite a few buildings and relocating thousands of graves.
So: His grave may not have received Ehrengrab-status and may no longer exist?