Owen Van Natta quietly resigned his position as Zynga’s executive vice president and chief business officer, a move made public by Amendment No. 6  Zynga filed yesterday to its Securities and Exchange Commission documents as it prepares for an initial public offering. He will remain on the Zynga board and serve the company in an advisory role, but Van Natta’s decision means he surrenders 4.64m share options.

The SEC document also reported that Spring Ventures founding partner Sunil Paul has joined the board, replacing Foundry Group managing director Brad Feld.

Details of the salary, bonuses, stock grants and options Van Natta received should cushion his transition, since they total more than $28 million according to the Los Angeles Times’ calculations.

Van Natta, former chief executive of Myspace and chief operating officer of Facebook, officially joined Zynga on August 16, 2010. His Zynga avatar (pictured right) and biography is still on the company’s page as of this writing, which further indicates the low-key and unexpected nature of his resignation.

Zynga, whose games include the hugely popular Zynga Poker, Mafia Wars and the “Ville” franchise of FarmVille, CityVille and CastleVille, additionally reported having 3.4 million paying customers – not including the multitudes who play for free – in the quarter that ended in September.

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