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If a domain was purchased from a registrar A but the DNS settings for that registrar point to Amazon, where do I edit the zone file in AWS? Do I have to create a new Hosted Zone or edit a zone file inside the Linux EC2 instance? Where do I find the file?

In the ubuntu machine there is no /etc/named.conf

Any idea where I can add my MX settings that the registrar provided? without impacting existing urls and dns settings and certificates?

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    Best to say what's the actual domain name - then we can tell where it is hosted, etc. Domains are public anyway, no need to try to keep the name from us if you need help. – MLu Aug 11 at 21:51
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In AWS's Route 53, you can create hosted zones, which is basically the logical equivalent of a zone file. You can modify it's entries via AWS's web console. Manually editing zones-files with a text-editor is not intended from AWS. No EC2-Instances or other servers need to be involved.

To make these hosted zones work for your domain, you must list AWS's DNS-Servers in your domain's NS-Record. When creating a hosted zone, it's NS-Records default to use AWS-DNS-Servers which can be used for this purpose.

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