Sergey

Переместил phpMyAdmin в папку www, назначил права, не помогло.
mv /usr/share/phpMyAdmin /var/www/phpMyAdmin
chown -R apache:apache /var/www/phpMyAdmin

/etc/nginx/conf.d

server {
        listen       80;
        server_name pma.site1.com;
        set $root_path /var/www/phpMyAdmin/;

        location / {
                root $root_path;
                index index.php;
        }
		
        location ~ \.php$ {
                fastcgi_pass 127.0.0.1:9000;
                fastcgi_index index.php;
                fastcgi_param SCRIPT_FILENAME $root_path$fastcgi_script_name;
                include fastcgi_params;
                fastcgi_param DOCUMENT_ROOT $root_path;
                fastcgi_read_timeout 300;
        }
}