This overall scene is actually composed of three separate sections:

• The longest sequence takes place at a restaurant, "Ruthie's Skillet Diner", where Skye pretends she is trying to decrypt a hard drive for Ward, but is actually stalling for time until she is rescued.
  
  
• That diner sequence is preceded by a scene of Skye & Ward walking along the street, talking, on their way to the restaurant.
  
  
• And the diner scene is followed by Sky's attempt to escape, only to be attacked by Mike Petersen (AKA "Deathlok").
  

We have seen Ruthie's Skillet Diner before.

It was where Skye first met Mike Petersen, way back in the pilot Episode 1,
when Skye was just a rebellious hacker, before she had joined S.H.I.E.L.D.

(You can read all about it here.)

This new scene was shot in the exact same location as that original scene from the pilot:
 inside a real restaurant in L.A.'s Chinatown.  But it's not really named Ruthie's Skillet.

This is the actually "Spring Street Smoke House Barbecue", a Southern style rib joint
at 640 N. Spring Street, which is just northwest of L.A.'s historic Olvera Street,
on the east end of Chinatown, in downtown Los Angeles,

(You'll find the restaurant's website here.)

Here is a Google StreetView of the location.

         

The earlier scene, of Skye & Ward walking to the restaurant,
was shot on Spring Street, just north of the diner.

They are walking south, along the east side of the street, in the
650 block of North Spring Street, in Chinatown.  They changed a
few storefront signs, but otherwise, it looks basically the same in real life.

Here is a Google StreetView of where they walked.

         

And the final scene of Skye trying to escape (and being captured by Deathlok)?

That was also shot on Spring Street, first right in front of the diner, when Skye is dealing
with the police, and then later, as Skye drives off in a cop car, we move a bit farther to
the north, around 680 N. Spring Street, with the car driving north/northeast.

(That hill you see in the distance is a bit of Elysian Park, next to Dodger Stadium.

They tinkered a bit with some of the distant buildings, behind Deathlok
as he jumps (for CGI purposes), but otherwise it's just Spring Street.

Here is a matching StreetView of the street, looking north.