Where can I apply for health certificate, physical examination and residence permit?

You can't.

Must be a valid residence permit at the place of residence.

To apply for a health certificate, you must have the original ID card. The residence permit is only a proof that you can live in the local area and has no other legal effect. Can't be used instead of ID card. To apply for a health certificate, you only need to provide relevant documents to the local CDC or the physical examination department of the hospital and explain that you can apply for a health certificate.