If you have ever used cPanel, there may have been a time that a DNS zone was missing even though your domain was already added on. If you have root access, you are able to fix this by using the adddns script. This is located in the /scripts directory, but only if you are using cPanel. So to use this, you will define the domain and the IP that it is for.
/scripts/adddns --domain=site.com --ip=123.456.7.89
That will create a dns zone for the domain site.com with the address on the server of 123.456.7.89. You can then check /var/named/site.com.db to make sure that it created successfully.