var index = items.indexOf(3452);

if (index !== -1) {
    items[index] = 1010;
}

Also it is recommend you not use the constructor method to initialize your arrays. Instead, use the literal syntax:

var items = [523, 3452, 334, 31, 5346];

You can also use the ~ operator if you are into terse JavaScript and want to shorten the -1 comparison:

var index = items.indexOf(3452);

if (~index) {
    items[index] = 1010;
}

Sometimes I even like to write a contains function to abstract this check and make it easier to understand what's going on. What's awesome is this works on arrays and strings both:

var contains = function (haystack, needle) {
    return !!~haystack.indexOf(needle);
};

// can be used like so now:
if (contains(items, 3452)) {
    // do something else...
}

Starting with ES6/ES2015 for strings, and proposed for ES2016 for arrays, you can more easily determine if a source contains another value:

if (haystack.includes(needle)) {
    // do your thing
}