there is no possibility to assign a cost center to the material master or to assign a plant to the cost center master data in the SAP Standard.
The field WERKS is available in the cost center master data table CSKS but it is not used anymore. Field WERKS is a relict of R/2. In R/2 cost centers are defined as WERKS/KOSTL, for instance 01/0000004711. In the beginning of development of R/3 at the end of the eightiees the design of CSKS was made including the WERKS field because it wasn't clear if we will need it for migration R2 ==> R3 or not.
Finally the field is unused till now and there's no plan to use it in
You can use it on your own risk with modifying the KS01/2/3 screens and implementing the user exit COOMKS01 which allows the use of addtitional fields.
Hope this helps.