FAQ PAGE

What is the Metal MACiE DB intended for?
The Metal MACiE database has the purpose of annotating both the properties and the functions of the metal ions involved in the catalytic mechanism of enzymes. The database is an extension of the MACiE database and is the result of a collaborative project among three institutes: the Magnetic Resonance Center (University of Florence), the European Bioinformatics Institute and the Unilever Center (University of Cambridge). The metal ions involved in structural roles are not annotated in the Metal MACiE DB.
How do I query the Metal MACiE DB?
You can query the database from its home page or using the advanced query page. Each field in the query form is linked to an onmouseover event which visualizes a description that hopefully will give you some more information on how to use it. If you have never heard about onmouseover events, please move your mouse on a specific field and look what happens. If you fill more than one field in the form, the database will be searched for enzymes which satisfy all the required features.
What type of information can I find in the Metal MACiE DB?
Here is a list of all the information that you can find in Metal MACiE:

... On the enzyme:
1- Enzyme name.
2- MACiE reference code.
3- Active Site Location of the enzyme (interface or core).
4- Catalytic Metal(s) contained in the enzyme on the basis of the MACiE database (Metal(s) are called using the MACiE reference structure as "Metal name in pdb"_"Metal number in pdb"_"Metal chain" e.g. CU_502_A).
5- Physiological catalytic metals on the basis of the literature.

...On each metal of a selected enzyme (overall reaction or sigle reaction step as annotated in MACiE):
1- The site type or the cofactor it belongs to (dinuclear, haem, etc.)
2- A representative structure of the intermediates (including the resting state).
3- The oxidation state of the metal.
4- The coordination geometry.
5- The coordination number.
6- Residues and/or exogenous ligands for the metal.
7- The metal function(s).
8- References for the metal function(s).
How is information organized in the Metal MACiE DB interface?
All the information on a metalloenzyme annotated in the Metal MACiE DB is organized in 4 different types of web pages (N.B. Most of the links in Metal MACiE DB are in green):

1-Entry home Page This page is intended to give general information on the metalloenzyme and some details on its resting state. One home page is associated to each metalloenzyme.

2-Step info page This page is intended to give a detailed information on the metal(s) properties and function(s) in the step under analysis. For each metalloenzyme, the number of step info pages is the same as the number of reaction steps annotated in MACiE. To access these pages, from any page click on "Step n" buttons in the "Browse reaction info" section (on the left).

3-First coordination sphere page This page is intended to give detailed information on the first coordination sphere of each metal in each reaction step (including the resting state). This page is available only if a representative pdb structure of the relevant intermediate is available. To access the resting state coordination info, from the Entry home page click on the "Resting state enzyme" button in the "Catalytic metal(s)" section. To access the coordination info for each page, from each Step info page click on the "Substrate-bound" or "Product-bound" button in the "Catalytic Metal(s) in Step n" section.

4- Metal info page This page is intended to give detailed information on each metal ion in the resting state and at all steps of the reaction. For each metalloenzyme, the number of Metal info pages is the same as the number of catalytic metal ions bound to the enzyme.
Where is the information of the Metal MACiE DB extracted from?
The information in the Metal MACiE DB is based on the available literature and is manually filled using a web interface. The first coordination sphere information has been automatically extracted from a representative pdb structure. The database is manually curated.
How polynuclear clusters are treated in the Metal MACiE DB?
All the metals belonging to a polynuclear site are treated separately except in case of iron-sulfur clusters, which are annotated as units. For iron-sulfur clusters, the oxidation state refers to the global charge of the cluster whereas the coordination number and geometry refer to each iron ion in the cluster.
How to move from an entry in Metal-MACiE to the corresponding entry in MACiE?
Entry pages of MACiE can be accessed by clicking on the MACiE ID number, which is present at the top of all Metal-MACiE pages, or on the "Overall reaction" link, which is present at the top of every entry page of Metal-MACiE. Also, reaction step pages of MACiE can be accessed from the corresponding Metal-MACiE reaction step pages by clicking on the "Step [Step number]" link.
How to return from a specific results page to the home search page?
The Metal-MACiE logo, in the top left corner, is a link to the Metal-MACiE home page.