Satellite images at Google Earth helped identify several ABM interceptor sites located around Moscow. Unfortunately, only short-range interceptor site are close enough to the city to get inside the high-resolution area. Here they are:
These are short-range 53T6 interceptors - 68 of them overall. These are probably all 53T6 that are out there. Mikhail Pervov in his book on Soviet missile and space defense mentiones this number when he describes the A-135 system (p. 244 of the 1st edition). Pervov, however, describes an early draft of the system design - ca. 1974. In this draft, short-range interceptors were grouped in four groups of 16 missiles and one, which would protect the Don-2N radar - of four. As we can see from the today's configuration, the plans have changed - the battery in Sofrino, which defends the radar, includes 12 interceptors. Still, it is likely that the overall number of short-range interceptors stayed the same.
The situation with long-range interceptors is more complex. According to the 1974 plan they were to be deployed in four groups of eight missiles. In addition to this, we know that the new missiles (51T6) used the sites that were left from old A-350/Galosh interceptors of the A-35 system. What we don't know is which ones were used - there are only 32 51T6 missiles, while there were 64 A-350 interceptors. The latter were deployed at four sites, each of which included two missile systems - either Yenisey or a slightly more advanced Tobol. Each system included eight interceptors, so there were 16 missiles per site.
The four sites in question were Zagorsk/Sergiyev Posad (Tobol and Yenisey systems), Klin (Tobol and Yenisey), Naro-Fominsk (Tobol and Yenisey), and Nudol (two Tobols). It is tempting to suggest that newer 51T6 missiles were deployed at all four sites, exactly as it was specified in the 1974 plan. But more recent accounts (for example, an article in NVO and a number of other sources) describe only seven interceptor sites of the A-135 system. Nobody ever mentioned nine sites. This means that two of the A-35 sites may have been abandoned.
The two-site hypothesis is also supported by the fact that the units of the 9th missile defense division, which operates the A-135 system, are stationed in two cities – Naro-Fominsk-10 (Vostochnyy, Moskovskaya oblast) and Sergiyev Posad-15 (Zhuklino, Vladimirskaya oblast). There seem to be no units in Klin or Nudol.
There are indeed interceptor positions near Naro-Fominsk-10 and Sergiyev Posad-15, but these could be old abandoned positions of the A-35 system (here is a set of interesting photos from the Zhuklino site near Sergiyev Posad-15). Because of the low resolution, it is difficult to say if there are 51T6 interceptors there.
The bottom line is that there seem to be two units that operate long-range 51T6 missiles and these are located in Naro-Fominsk-10 and Sergiyev Posad-15, but it is hard to say where the interceptor silos are located and how many sites are there. We may have to wait until Google posts high-resolution data of the area.
A .kml file with the sites mentioned in this post is here. An ineresting discussion of Moscow ABM sites with some .kmz files can be found at a bbs.keyhole.com forum. My thanks to the forum contributors for providing very useful insights.