Dear Goyal
yes u can bind the mqSeries com.ibm.mq.jms.MQXAQueueConnectionFactory and MqSeries Queue in the jndi and if u lookup from any java code u can directly access the MQSeries.U can refer the following code for binding

factory = new MQXAQueueConnectionFactory();
(factory).setQueueManager(QMGR);
// factory.setTransportType(1);

connection = factory.createXAQueueConnection();

connection.start();

boolean transacted = false;
//session = connection.createXAQueueSession(true,Session.AUTO_ACKNOWLEDGE);
session = connection.createXAQueueSession();

QueueSession s = session.getQueueSession();
ctx.bind("BindedQueueConnectionFactory",factory);
ctx.bind("BindedQueue",ioQueue);