Can I enroll to graduate school (PhD) in Germany? I'm finishing Masters degree in Computer Engineering at university of Russia in this year. GPA of my Master diploma is 4.9-4.0 from 5. I have 3 publications in russian scientific journals. However, my bachelor's GPA is 3.5 from 5 and I think it is main problem for enrolling to PhD. My past low level of Bachelor's degree correlated with the lack of interest in Science. At the moment my interest in Science growing more and more, than more I understand in the research. I'm studying some courses on educational platforms such as Coursera and edX for to correct my past mistakes and for increase my scientific outlook.

Do I have any chances for enrolling to PhD in Germany? I don't pretend to top universities.
The formal requirement for enrolling as a PhD student at a German university will typically be to have a Master's degree, potentially with some (modest) grade requirements (on the Master's, the Bachelor wouldn't matter); and to obtain the agreement of a Professor to act as your PhD supervisor. The latter of course is a very individual decision.